{"text": "pneumoniae</i> NTUH-K2044 by analyzing the virulence plasmid structure.<h4>Conclusion</h4>Our results suggest that the gut colonized ST11 hv-CRKP may serve as a reservoir for the clinical pathogenic ST11 HV-CRKP. It is necessary to further strengthen the monitoring of gut colonized hv-CRKP and research the potential mechanism of infection caused by gut colonized hv-CRKP.\n\nComparative Genomic Analysis of Hypervirulence Carbapenem-Resistant <i>Klebsiella pneumoniae</i> from Inpatients with Infection and Gut Colonization, China.", "token_count": 165, "char_count": 531, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": {"genes": ["ST11"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:51.876199", "source": {"split": "train_shard_00001", "doc_id": 597}, "chunk_id": "train_shard_00001_597_1", "global_id": 6500}
{"text": "Structure and conformational behaviour of a putative β-1,4-glucosidase of glycoside hydrolase family 3 (PsGH3) from Pseudopedobacter saltans was predicted by using in-silico tools. PsGH3 modeled structure constructed using Phyre2 displayed multidomain architecture comprising an N-terminal (β/α)<sub>8</sub>-fold domain followed by (α/β)<sub>6</sub>-sandwich domain, PA14 domain, and a C-terminal domain resembling an immunoglobulin fold. Ramachandran plot displayed 99.3% of amino acids in the allowed region and 0.7% residues in the disallowed region. Multiple sequence alignment (MSA) and structure superposition of PsGH3 with other homologues from GH3 family revealed the conserved residues, Asp274 and Glu624 present in loops LA and LB, respectively originating from N-terminal domain act as catalytic residues. The volume and area calculated for PsGH3 displayed a deep active-site conformation comparable with its homologues, β-1,4-glucosidases (GH3) of Kluyveromyces marxianus and Streptomyces venezuelae. Molecular dynamic (MD) simulation of PsGH3 structure for 80 ns suggested stable and compact structure. Molecular docking studies revealed deeper active site conformation of PsGH3 that could house larger cellooligosaccharides up to 7° of polymerization (DP7). The amino acid residues, Ala86, Leu88, Cys275, Pro483, Phe493, Asn417, Asn491, Pro492, and Leu495 created a binding pocket near the catalytic cleft, crucial for ligand binding. MD simulation of PsGH3 in the presence of cellooligosaccharides, viz., cellobiose and celloheptaose showed stability in terms of RMSD, R<sub>g</sub>, and SASA values till 80 ns", "token_count": 516, "char_count": 1625, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": {"genes": ["GH3", "DP7", "PA14"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces"], "conditions": ["acid", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:43:52.481750", "source": {"split": "train_shard_00001", "doc_id": 598}, "chunk_id": "train_shard_00001_598_0", "global_id": 6501}
{"text": "The calculation of average number of hydrogen bond (H-bond), interaction energy, and binding free energy confirmed the stronger binding affinity of the larger cellooligosaccharides such as celloheptaose in the binding cavity of PsGH3.\n\nStructure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans.", "token_count": 108, "char_count": 381, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:52.854590", "source": {"split": "train_shard_00001", "doc_id": 598}, "chunk_id": "train_shard_00001_598_1", "global_id": 6502}
{"text": "<h4>Objectives</h4>This is the first study conducted in southern Spain to determine i) the population structure (PS) of carbapenem-resistant (CR) Acinetobacter baumannii isolates by multilocus sequencing typing (MLST) and core genome MLST (cgMLST) and ii) the association between the sequence type ST and the bla<sub>OXA-51</sub> variant, capsule polysaccharide locus (KL) and lipooligosaccharide outer core locus (OCL) types.<h4>Methods</h4>Of 336 isolates submitted to the Andalusian reference laboratory (PIRASOA; December 2017-2020), 73 were subjected to WGS (MiSeq). The following analyses were performed: bacterial identification (ribosomal MLST), carbapenemase gene detection (Resfinder 4.0), PS delineation (MLST by MLSTfinder 2.0 and cgMLST by Ridom SeqSphere<sup>+</sup>), and KL types and OCL types (Kaptive tool).<h4>Results</h4>The carbapenemases detected were bla<sub>OXA-23</sub> (n = 41), bla<sub>OXA-58</sub> (n = 26), bla<sub>OXA-24</sub> (n = 5), bla<sub>OXA-72</sub> (n = 1) and bla<sub>NDM-1</sub> (n = 2). The PS revealed one major ST2 clone (n = 54) and seven minor ST clones by MLST, and 41 lineages by cgMLST<sub>.</sub> Thirty-five lineages were detected only in a single hospital whereas five lineages were observed in several hospitals and provinces", "token_count": 485, "char_count": 1277, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": {"genes": ["ST2"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:53.478302", "source": {"split": "train_shard_00001", "doc_id": 599}, "chunk_id": "train_shard_00001_599_0", "global_id": 6503}
{"text": "bla<sub>OXA-66</sub> was the most frequent bla<sub>OXA-51</sub> variant and was mainly associated with the ST2 clone. Eleven KL types and 3 OCL types were assigned, with KL2 (n = 27), KL7 (n = 16) and OCL1 being the most frequent.<h4>Conclusions</h4>The PS of CR A. baumannii in Andalusia is characterized by a dominant ST2/bla<sub>OXA-23</sub> clone and several lineages, showing local spread of lineages in most hospitals, and intercenter or interregional spread of a few lineages. Single-locus bla<sub>OXA-51-like</sub> typing and KL typing may be useful as complementary preliminary typing tool.\n\nRegional distribution of carbapenemase-producing Acinetobacter baumannii isolates in southern Spain (Andalusia).", "token_count": 243, "char_count": 713, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7449, "quality_score": 0.8724, "entities": {"genes": ["OCL1", "KL7", "ST2", "KL2"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:53.938694", "source": {"split": "train_shard_00001", "doc_id": 599}, "chunk_id": "train_shard_00001_599_1", "global_id": 6504}
{"text": "Thirty-three <i>Kluyveromyces marxianus</i> strains were tested for the ability to form biofilm and mat structures in YPD and whey and for cell surface hydrophobicity. To identify genes potentially involved in adhesion properties, a RT-qPCR analysis was performed. Eight strains were able to adhere on polystyrene plates in both media and formed a mature mat structure. These strains showed a different level of hydrophobicity ranging from 55 to 66% in YPD and from 69 to 81% in whey. Four <i>K. marxianus</i> orthologs genes (<i>FLO11</i>, <i>STE12</i>, <i>TPK3</i>, and <i>WSC4</i>), known from studies in other yeast to be involved in biofilm formation, have been studied. <i>FLO11</i> and <i>STE12</i> showed the highest fold changes in all conditions tested and especially in whey: 15.05 and 11.21, respectively. <i>TPK3</i> was upregulated only in a strain, and <i>WSC4</i> in 3 strains. In YPD, fold changes were lower than in whey with <i>STE12</i> and <i>FLO11</i> genes showing the highest fold changes. In mat structures <i>FLO11</i> and <i>STE12</i> fold changes ranged from 3.6-1.3 to 2-1.17, respectively. Further studies are necessary to better understand the role of these genes in <i>K. marxianus</i> adhesion ability.\n\nCell Wall Surface Properties of <i>Kluyveromyces marxianus</i> Strains From Dairy-Products.", "token_count": 445, "char_count": 1328, "word_count": 194, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": {"genes": ["TPK3", "FLO11", "STE12", "WSC4"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:54.544218", "source": {"split": "train_shard_00001", "doc_id": 600}, "chunk_id": "train_shard_00001_600_0", "global_id": 6505}
{"text": "To overcome the economic losses associated with fungi and their toxic metabolites, environmentally safe and efficient approaches are needed. To this end, biological control using yeasts and safe bacterial strains and their products are being explored to replace synthetic fungicides. In the present study, the biocontrol effect of a yeast strain of <i>Kluyveromyces marxianus</i>, QKM-4, against the growth and mycotoxin synthesis potential of key toxigenic fungi was evaluated. <i>In vitro</i> assays were performed to find the application of yeast volatile organic compounds (VOCs) against fungal contamination on important agricultural commodities. The removal of ochratoxin A (OTA) and deoxynivalenol (DON) by living and heat-inactivated yeast cells was also explored. VOCs produced by strain QKM-4 were able to significantly limit the fungal growth of 17 fungal species belonging to genera <i>Aspergillus</i>, <i>Penicillium</i>, and <i>Fusarium</i>. Yeast VOCs were able to reduce OTA biosynthesis potential of <i>Penicillium verrucosum</i> and <i>Aspergillus carbonarius</i> by 99.6 and 98.7%, respectively. <i>In vivo</i> application of QKM-4 VOCs against <i>Fusarium oxysporum</i> and <i>A. carbonarius</i> infection on tomatoes and grapes, respectively, determined a complete inhibition of fungal spore germination. GC/MS-based analysis of yeast VOCs identified long-chain alkanes, including nonadecane, eicosane, docosane, heptacosane, hexatriacontane, and tetracosane. <i>In vitro</i> testing of the mycotoxin-binding potential of the living and heat-inactivated QKM-4 cells showed a reduction of OTA and DON up to 58 and 49%, respectively, from artificially contaminated buffers. Our findings clearly demonstrate the strong antifungal potential of <i>K", "token_count": 518, "char_count": 1765, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": []}, "biobert_ready": false, "timestamp": "2025-10-31T21:43:55.493674", "source": {"split": "train_shard_00001", "doc_id": 601}, "chunk_id": "train_shard_00001_601_0", "global_id": 6506}
{"text": "marxianus</i> QKM-4 and propose this strain as a strong candidate for application in agriculture to safeguard food and feed products.\n\nIsolation of a Novel <i>Kluyveromyces marxianus</i> Strain QKM-4 and Evidence of Its Volatilome Production and Binding Potentialities in the Biocontrol of Toxigenic Fungi and Their Mycotoxins.", "token_count": 102, "char_count": 327, "word_count": 46, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:55.860787", "source": {"split": "train_shard_00001", "doc_id": 601}, "chunk_id": "train_shard_00001_601_1", "global_id": 6507}
{"text": "The sunflower, an important oilseed crop and food source across the world, is susceptible to several pathogens, which cause severe losses in sunflower production. The utilization of genetic resistance is the most economical, effective measure to prevent infectious diseases. Based on the sunflower pangenome, in this study, we explored the variability of resistance gene analogs (RGAs) within the species. According to a comparative analysis of RGA candidates in the sunflower pangenome using the RGAugury pipeline, a total of 1344 RGAs were identified, comprising 1107 conserved, 199 varied, and 38 rare RGAs. We also identified RGAs associated with resistance against <i>Sclerotinia sclerotiorum</i> (<i>S. sclerotiorum</i>) in sunflower at the quantitative trait locus (QTL). A total of 61 RGAs were found to be located at four quantitative trait loci (QTLs). Through a detailed expression analysis of RGAs in one susceptible and two tolerant sunflower inbred lines (ILs) across various time points post inoculation, we discovered that 348 RGAs exhibited differential expression in response to Sclerotinia head rot (SHR), with 17 of these differentially expressed RGAs being situated within the QTL regions. In addition, 15 RGA candidates had gene introgression. Our data provide a better understanding of RGAs, which facilitate genomics-based improvements in disease resistance in sunflower.\n\nPangenome Data Analysis Reveals Characteristics of Resistance Gene Analogs Associated with <i>Sclerotinia sclerotiorum</i> Resistance in Sunflower.", "token_count": 410, "char_count": 1544, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8196, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:56.458643", "source": {"split": "train_shard_00001", "doc_id": 602}, "chunk_id": "train_shard_00001_602_0", "global_id": 6508}
{"text": "<h4>Background</h4>Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database.<h4>Results</h4>Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes.<h4>Conclusions</h4>Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.", "token_count": 511, "char_count": 1794, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5661, "quality_score": 0.7831, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:57.089199", "source": {"split": "train_shard_00001", "doc_id": 603}, "chunk_id": "train_shard_00001_603_0", "global_id": 6509}
{"text": "Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces.", "token_count": 36, "char_count": 150, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:57.441336", "source": {"split": "train_shard_00001", "doc_id": 603}, "chunk_id": "train_shard_00001_603_1", "global_id": 6510}
{"text": "<h4>Background</h4> The new complete telomere-to-telomere human genome assembly, T2T-CHM13, and the first draft of the human pangenome reference provide unique opportunities to update the reference genome for epigenetics investigations and clinical research. However, it is largely unclear how these reference genome updates may impact DNA methylation (DNAm) analysis. <h4>Results</h4> Compared to the previous GRCh38 assembly, we found an average increase of 7.4% (range 5.4%–9.9% across samples and sequencing methods) in the number of CpGs genome-wide using T2T-CHM13 with data from four commonly used short-read sequencing DNAm profiling methods. The increase in number of CpGs facilitated discovery of 88 new differentially methylated CpGs within cancer driver genes in an epigenome-wide association study (EWAS) of colon cancer. Further, by aligning probe sequences from the commonly used and recently released Illumina DNAm arrays to T2T-CHM13 and GRCh38, we showed the enhanced utility of T2T-CHM13 for evaluation of potential probe cross-reactivity (i.e., where probes match multiple regions) and mismatch (i.e., where probes do not perfectly match the target region), resulting in the identification of new and more reproducible sets of unambiguous probes (i.e., probes uniquely mapping to the target region) (HM450K, n = 430,719; EPIC, n = 777,491; EPICv2, n = 859,216). In EWASs of 24 cancer types, an average of 945 additional differentially methylated CpG sites were identified in the new unambiguous probe set rather than in the GRCh38-based unambiguous probe set, with enrichments in cancer driver genes and cancer signaling pathways", "token_count": 469, "char_count": 1649, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": {"genes": ["HM450K", "CHM13"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:58.053802", "source": {"split": "train_shard_00001", "doc_id": 604}, "chunk_id": "train_shard_00001_604_0", "global_id": 6511}
{"text": "Moreover, the pangenome called 4.5% more CpGs on average in short-read sequencing data than T2T-CHM13 and identified cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These additional CpGs were overlapped with the promoters and gene bodies of various biologically and medically relevant genes and pangenome-based unambiguous probes can potentially facilitate the discovery of DNAm alterations in more than 200 cancer driver genes in each cancer type. <h4>Conclusions</h4> Use of T2T-CHM13 and pangenome references can benefit epigenome-wide association studies by including CpGs previously unobserved in short-read sequencing data and by improving the identification of unambiguous probes for DNAm arrays, thus expanding biologically relevant information. This study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of epigenetics investigations.\n\nComplete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array Data", "token_count": 276, "char_count": 1167, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8105, "entities": {"genes": ["CHM13"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:58.581724", "source": {"split": "train_shard_00001", "doc_id": 604}, "chunk_id": "train_shard_00001_604_1", "global_id": 6512}
{"text": "<h4>Background</h4> The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit the underlying optimization criterion and the set of feasible solutions. Current approaches build a pangenome graph with some heuristics, without assuming some explicit optimization criteria. Thus it is unclear how a specific optimization criterion affects the graph topology and downstream analysis, like read mapping and variant calling. <h4>Methods</h4> In this paper, by leveraging the notion of maximal block in a Multiple Sequence Alignment (MSA), we reframe the pangenome graph construction problem as an exact cover problem on blocks called Minimum Weighted Block Cover (MWBC). Then we propose an Integer Linear Programming (ILP) formulation for the MWBC problem that allows us to study the most natural objective functions for building a graph. <h4>Results</h4> We provide an implementation of the ILP approach for solving the MWBC and we evaluate it on SARS-CoV-2 complete genomes, showing how different objective functions lead to pangenome graphs that have different properties, hinting that the specific downstream task can drive the graph construction phase. <h4>Conclusion</h4> We show that a customized construction of a pangenome graph based on selecting objective functions has a direct impact on the resulting graphs. In particular, our formalization of the MWBC problem, based on finding an optimal subset of blocks covering an MSA, paves the way to novel practical approaches to graph representations of an MSA where the user can guide the construction.\n\nPangeBlocks: customized construction of pangenome graphs via maximal blocks", "token_count": 388, "char_count": 1780, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:59.174083", "source": {"split": "train_shard_00001", "doc_id": 605}, "chunk_id": "train_shard_00001_605_0", "global_id": 6513}
{"text": "The aim of the study was to evaluate the impact of probiotics obtained from agro-industrial substrates fermented with lactic acid bacteria and/or yeasts on the health and changes in the microbiota of the digestive tract of guinea pigs. Eighty male guinea pigs, Kuri breed, 30 days old and 250 g live weight, were randomly selected and divided into four groups of 20 animals each. T0, Control, T1, Lactobacillus acidophilus and L. bulgaricus. T2, Saccharomyces cerevisiae and Kluyveromyces fragilis and T3. L acidophilus, L bulgariccus, S cerevisiae and K. fragilis. T1, T2 and T3 contained molasses-vinasse substrate in their base, the dose administered was 0.75 mL/animal orally. The parameters evaluated were weight gain, occurrence of diarrhea and mortality, blood profile, macroscopic lesions in the digestive tract organs and changes in the microbiota of the stomach, caecum, small and large intestine. Treatments T1, T2 and T3 improved weight gain (p&lt;0.05) and reduced the presence of guinea pigs with diarrhea (p&lt;0.05) and there was no mortality; hematic indices did not vary significantly (p&gt;0.05) between treatments; animals in the control group presented a greater amount (p&lt;0.05) of macroscopic lesions in the digestive tract organs; in the T1, T2 and T3 group there was an improvement in the natural microbiota. It is concluded that the inclusion of microbial additive in young guinea pigs improves intestinal health, consequently, improves weight gain, reduces diarrhea and deaths, and normalizes the natural microbiota of the gastrointestinal tract.\n\nEffect of Agro-Industrial Substrates Fermented with Lactic Acid Bacteria and Yeasts on the Intestinal Microbiota of Guinea Pigs (Cavia porcellus)", "token_count": 497, "char_count": 1722, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["kluyveromyces", "yeast", "saccharomyces"], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:43:59.793736", "source": {"split": "train_shard_00001", "doc_id": 606}, "chunk_id": "train_shard_00001_606_0", "global_id": 6514}
{"text": "<h4>ABSTRACT</h4>  The 17q21.31 locus in humans harbors several complex structural haplotypes including a ∼970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is ∼2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the KANSL1 gene which may predispose them to Koolen-de Vries syndrome causing microdeletions. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in ∼5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased ∼6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.\n\nRecurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes", "token_count": 449, "char_count": 1738, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": {"genes": ["KANSL1"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:00.408000", "source": {"split": "train_shard_00001", "doc_id": 607}, "chunk_id": "train_shard_00001_607_0", "global_id": 6515}
{"text": "Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae , then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus , unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses. <h4>Importance</h4> Metagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA, and how much this impacts downstream analyses has not been studied", "token_count": 519, "char_count": 2315, "word_count": 322, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:01.065771", "source": {"split": "train_shard_00001", "doc_id": 608}, "chunk_id": "train_shard_00001_608_0", "global_id": 6516}
{"text": "Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged, and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.\n\nSmall amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses", "token_count": 142, "char_count": 623, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7907, "quality_score": 0.8953, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:01.498783", "source": {"split": "train_shard_00001", "doc_id": 608}, "chunk_id": "train_shard_00001_608_1", "global_id": 6517}
{"text": "Woody ornamentals are an integral part of home gardens and urban landscapes and are key to the economic vitality of the nursery industry. Movement of plants infected with emerging pathogens can quickly lead to wide geographic spread of new diseases impacting ecosystem health and leading to economic losses. Using metagenomic sequencing, we investigated the microbial species associated with vascular streak dieback (VSD), an emerging disease of woody ornamentals in the United States, analyzing 106 samples obtained from 34 different species in seven states. The fastidious fungal pathogen Ceratobasidium sp. ( Csp ), previously found to be associated with VSD, was the only putative pathogen consistently identified. Assembly of 17 high quality draft genomes followed by phylogenetic and pangenome analyses revealed Csp to form a tight genetic cluster closely related to, yet distinct in gene content, from genomes of Ceratobasidium theobromae , a pathogen of cacao, avocado, and cassava in Southeast Asia. These results reveal the unparalleled ability of metagenomics for identification and characterization of fastidious fungal pathogens and suggest the recent introduction of a single genetic lineage of Csp into the U.S., possibly from Southeast Asia, that is characterized by a wide host range and that quickly spread geographically.\n\nInsights gained into Vascular Streak Dieback, an Emerging Disease of Woody Ornamentals in the United States, using Metagenomic Sequencing", "token_count": 340, "char_count": 1479, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:02.078321", "source": {"split": "train_shard_00001", "doc_id": 609}, "chunk_id": "train_shard_00001_609_0", "global_id": 6518}
{"text": "The higher adaptation of landraces to local agroclimatic conditions resulting from natural and moderate artificial selection by farmers within specific environments makes them a crucial source of alleles and genotypes for cultivation and breeding programs. Unlike modern cultivars, which have been developed under more intense artificial selective pressures, landraces exhibit a broader genetic base that has been documented in landrace collections for many crops. This review provides an overview of the importance of genetic resource valorisation in legume species, focusing on cultivated species of the <i>Lupinus</i> genus, particularly white lupin (<i>Lupinus albus</i>). On the one hand, legumes, including Lupins, are considered a crucial alternative source of protein within the framework of more sustainable agriculture. On the other hand, they are often neglected species in terms of breeding efforts, despite receiving increasing attention in recent years. Here, we also report on the latest advances in the development of genomic tools, such as the novel pangenome of white lupin and the identification of markers and loci for target adaptation traits, such as tolerance to alkaline soils, which can effectively support the breeding of <i>Lupinus albus</i>, especially for the introgression of desirable alleles from locally adapted varieties.\n\nRecent Advances in Molecular Tools and Pre-Breeding Activities in White Lupin (&lt;i&gt;Lupinus albus&lt;/i&gt;).", "token_count": 327, "char_count": 1470, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8357, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:02.652259", "source": {"split": "train_shard_00001", "doc_id": 610}, "chunk_id": "train_shard_00001_610_0", "global_id": 6519}
{"text": "Sustainable economy drives increasing demand for raw biomass-decomposing enzymes. Microbial expression platforms exploited as cellular factories of such biocatalysts meet requirements of large-volume production. Previously, we developed <i>Yarrowia lipolytica</i> recombinant strains able to grow on raw starch of different plant origin. In the present study, we used the most efficient amylolytic strain as a microbial cell factory of raw-starch-digesting (RSD) amylolytic preparation composed of two enzymes. The RSD-preparation was produced in fed-batch bioreactor cultures. Concentrated and partly purified preparation was then tested in simultaneous saccharification and fermentation (SSF) processes with thermotolerant <i>Kluyveromyces marxianus</i> for ethanol production and <i>Lactobacillus plantarum</i> for production of lactic acid. These processes were conducted as a proof-of-concept that application of the novel RSD-preparation supports sufficient starch hydrolysis enabling microbial growth and production of targeted molecules, as the selected strains were confirmed to lack amylolytic activity. Doses of the preparation and thermal conditions were individually adjusted for the two processes. Additionally, ethanol production was tested under different aeration strategies; and lactic acid production process was tested in thermally pre-treated substrate, as well. Conducted studies demonstrated that the novel RSD-preparation provides satisfactory starch hydrolyzing activity for ethanol and lactic acid production from starch by non-amylolytic microorganisms.\n\nProduction of Raw Starch-Digesting Amylolytic Preparation in <i>Yarrowia lipolytica</i> and Its Application in Biotechnological Synthesis of Lactic Acid and Ethanol.", "token_count": 436, "char_count": 1747, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces"], "conditions": ["acid"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:03.262032", "source": {"split": "train_shard_00001", "doc_id": 611}, "chunk_id": "train_shard_00001_611_0", "global_id": 6520}
{"text": "As the name of the genus <i>Pantoea</i> (\"of all sorts and sources\") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus <i>Pantoea</i>. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.\n\nGenomic delineation and description of species and within-species lineages in the genus &lt;i&gt;Pantoea&lt;/i&gt;.", "token_count": 369, "char_count": 1639, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6724, "quality_score": 0.8362, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:03.824114", "source": {"split": "train_shard_00001", "doc_id": 612}, "chunk_id": "train_shard_00001_612_0", "global_id": 6521}
{"text": "Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect Ablp eyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px 1 ) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c 1 ) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck . We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila .", "token_count": 511, "char_count": 1909, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6915, "quality_score": 0.8457, "entities": {"genes": ["DM412"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:04.443278", "source": {"split": "train_shard_00001", "doc_id": 613}, "chunk_id": "train_shard_00001_613_0", "global_id": 6522}
{"text": "Structural variants are enriched in deleterious visible phenotypes in <i>Drosophila</i>", "token_count": 28, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:04.788287", "source": {"split": "train_shard_00001", "doc_id": 613}, "chunk_id": "train_shard_00001_613_1", "global_id": 6523}
{"text": "<h4>Background</h4>Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.<h4>Methods</h4>Antimicrobial susceptibility testing was performed to determine resistance profiles using minimum inhibitory concentrations. Whole-genome sequencing was used to identify β-lactamase, carbapenemase, and other antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs). Clonal relationships among isolates were assessed via core genome multilocus sequence typing (cgMLST).<h4>Results</h4>Phenotypic analysis revealed that 72% of the isolates were extensively drug-resistant (XDR), exhibiting resistance to all tested antibiotics except colistin. Clonal diversity analysis identified 11 Oxford sequence types (STs), including two novel STs (ST3309<sup>OXF</sup> and ST3321<sup>OXF</sup>), and six international clonal (IC) groups, with IC2 being the most prevalent. Additionally, eight Pasteur STs were detected, with ST570<sup>PAS</sup> being the most frequent. The cgMLST analysis showed that two Egyptian ST570<sup>PAS</sup> isolates clustered with a strain from Saudi Arabia, suggesting potential regional transmission. Genomic analysis revealed the widespread dissemination of ARGs via MGEs, particularly rep plasmids and insertion sequence elements, which contributed significantly to genomic diversity and antibiotic resistance.<h4>Conclusions</h4>This pilot study highlights the clonal diversity of A. baumannii in Egypt and underscores the critical role of MGEs in the spread of resistance genes", "token_count": 515, "char_count": 2023, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": {"genes": ["IC2", "ST3309", "ST570", "ST3321"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:05.392157", "source": {"split": "train_shard_00001", "doc_id": 614}, "chunk_id": "train_shard_00001_614_0", "global_id": 6524}
{"text": "Targeted genomic surveillance and infection control are essential to curb the spread of high-risk resistant A. baumannii clones in Egyptian clinical settings.\n\nComparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization.", "token_count": 67, "char_count": 300, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:05.756473", "source": {"split": "train_shard_00001", "doc_id": 614}, "chunk_id": "train_shard_00001_614_1", "global_id": 6525}
{"text": "<h4>Background</h4>Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution.<h4>Results</h4>Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes.<h4>Conclusions</h4>Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.\n\nPangenome analysis reveals transposon-driven genome evolution in cotton.", "token_count": 473, "char_count": 1971, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:06.375103", "source": {"split": "train_shard_00001", "doc_id": 615}, "chunk_id": "train_shard_00001_615_0", "global_id": 6526}
{"text": "According to the latest WHO estimates (2015) of the global burden of foodborne diseases, <i>Listeria monocytogenes</i> is responsible for one of the most serious foodborne infections and commonly results in severe clinical outcomes. The 2013 French MONALISA prospective cohort identified that women born in Africa has a 3-fold increase in the risk of maternal neonatal listeriosis. One of the largest <i>L. monocytogenes</i> outbreaks occurred in South Africa in 2017-2018 with over 1,000 cases. Moreover, recent findings identified <i>L. monocytogenes</i> in human breast milk in Mali and Senegal with its relative abundance positively correlated with severe acute malnutrition. These observations suggest that the carriage of <i>L. monocytogenes</i> in Africa should be further explored, starting with the existing literature. For that purpose, we searched the peer-reviewed and grey literature published dating back to 1926 to date using six databases. Ultimately, 225 articles were included in this review. We highlighted that <i>L. monocytogenes</i> is detected in various sample types including environmental samples, food samples as well as animal and human samples. These studies were mostly conducted in five east African countries, four west African countries, four north African countries, and two Southern African countries. Moreover, only ≈ 0.2% of the <i>Listeria monocytogenes</i> genomes available on NCBI were obtained from African samples, contracted with its detection. The pangenome resulting from the African <i>Listeria monocytogenes</i> samples revealed three clusters including two from South-African strains as well as one consisting of the strains isolated from breast milk in Mali and Senegal and, a vaginal post-miscarriage sample. This suggests there was a clonal complex circulating in Mali and Senegal. As this clone has not been associated to infections, further studies should be conducted to confirm its circulation in the region and explore its association with foodborne infections. Moreover, it is apparent that more resources should be allocated to the detection of <i>L", "token_count": 511, "char_count": 2108, "word_count": 305, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:07.007992", "source": {"split": "train_shard_00001", "doc_id": 616}, "chunk_id": "train_shard_00001_616_0", "global_id": 6527}
{"text": "monocytogenes</i> as only 15/54 countries have reported its detection in the literature. It seems paramount to map the presence and carriage of <i>L. monocytogenes</i> in all African countries to prevent listeriosis outbreaks and the related miscarriages and confirm its association with severe acute malnutrition.\n\nA review of the literature of <i>Listeria monocytogenes</i> in Africa highlights breast milk as an overlooked human source.", "token_count": 113, "char_count": 439, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7581, "quality_score": 0.879, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:07.374703", "source": {"split": "train_shard_00001", "doc_id": 616}, "chunk_id": "train_shard_00001_616_1", "global_id": 6528}
{"text": "Pigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.\n\nPangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics", "token_count": 304, "char_count": 1359, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": {"genes": ["TBX19"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:07.920955", "source": {"split": "train_shard_00001", "doc_id": 617}, "chunk_id": "train_shard_00001_617_0", "global_id": 6529}
{"text": "<title>Abstract</title>  <p>Background: Lignocellulosic biomass is a promising renewable and sustainable resource for biofuels and chemicals. However, the inhibitors generated during lignocellulosic biomass pretreatment hinder microbial growth and interfere with fermentation. Studies on the tolerance to inhibitors, especially multiple inhibitors, are important in the construction of robust strains that can utilize lignocellulosic biomass. <h4>Results:</h4> The expression of an uncharted α/β hydrolase (ABHD) from <italic>Kluyveromyces marxianus</italic> was found to be up-regulated in the presence of single or multiple inhibitors; this enzyme was termed KmYME in this study. Disruption of KmYME made the yeast more susceptible to inhibitors, particularly to acetic acid, furfural and 5-hydroxymethylfurfural. KmYME was located in the mitoplast of mitochondria with targeting signals in the N-terminal 1-40 amino acid residues. Under inhibitor stress, the intracellular concentration of ATP, NAD(P) in the KmYME disrupted strain decreased. In addition, the KmYME disrupted strain lost more mitochondrial membrane potential, showed increased plasma membrane permeability, a more severe redox imbalance, and increased ROS accumulation, compared with those of the non-disrupted strain in the presence of the same inhibitors. The recombinant KmYME possessed esterase/thioesterase activity and preferred short-chain pNP aliphatic esters, long-chain acyl-CoA, and succinyl-CoA as substrates. The retro-complementation results indicated that the enzymatic activity of KmYME was necessary for the resistance to inhibitors. In addition, KmYME was also required for the resistance to other stresses including ethanol, temperature, and osmotic pressure. Disruption of two possible homologous genes in <italic>S. cerevisiae </italic>also reduced its tolerance to inhibitors", "token_count": 500, "char_count": 1867, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["acid", "ph", "temperature", "osmotic"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:08.543152", "source": {"split": "train_shard_00001", "doc_id": 618}, "chunk_id": "train_shard_00001_618_0", "global_id": 6530}
{"text": "<h4>Conclusion:</h4> As an uncharted α/β hydrolase, KmYME which had esterase/thioesterase activity and located in mitochondrial matrix was identified for the first time. The esterase/thioesterase activity was necessary for the tolerance to lignocellulosic biomass derived inhibitors in <italic>K. marxianus</italic>. Disruption of KmYME reduced the tolerance to inhibitors by interfering with ATP, NAD and NADP synthesis. KmYME also correlated with tolerance to other stresses such as osmotic, ethanol, and temperature. This study may provide useful information for better understanding the resistance mechanism of multiple inhibitors, which is important in the creation of a robust strain for industrial fermentation that can use cellulosic biomass as substrate.</p>\n\nEffect of a novel alpha/beta hydrolase domain protein on tolerance of K. marxianus to lignocellulosic biomass derived inhibitors", "token_count": 235, "char_count": 897, "word_count": 121, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus"], "conditions": ["ph", "temperature", "osmotic"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:08.997025", "source": {"split": "train_shard_00001", "doc_id": 618}, "chunk_id": "train_shard_00001_618_1", "global_id": 6531}
{"text": "<i>Pasteurella multocida</i> causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182-2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of <i>nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB</i>, and <i>omp87</i> in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters", "token_count": 491, "char_count": 1324, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7151, "quality_score": 0.8575, "entities": {"genes": ["ST13", "ST122", "ST50", "ST09", "ST07", "ST287", "ST74"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:09.618930", "source": {"split": "train_shard_00001", "doc_id": 619}, "chunk_id": "train_shard_00001_619_0", "global_id": 6532}
{"text": "In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of <i>P. multocida</i> of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.\n\nComparative genome analysis of <i>Pasteurella multocida</i> strains of porcine origin.", "token_count": 93, "char_count": 325, "word_count": 45, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:09.983002", "source": {"split": "train_shard_00001", "doc_id": 619}, "chunk_id": "train_shard_00001_619_1", "global_id": 6533}
{"text": "Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. However, the factors that influence the integration and long-term retention of transferred genes remain poorly understood. The pangenome of the grass Alloteropsis has a high turnover of laterally acquired genes, and here we combine expression, methylation and genomic data to identify factors promoting their long-term persistence. Most transferred genes appear to be degenerating, showing lower expression levels and/or greater sequence truncation compared to their vertically inherited homologs. These degenerating genes also show significantly higher levels of DNA methylation, potentially indicating transcriptional silencing. The likelihood of a transferred gene being retained will be influenced by how easily it can be expressed in the recipient genome. In Alloteropsis , putatively functional laterally acquired genes had expression levels significantly more similar to their donor xenolog than to their vertically inherited homolog. This pattern suggests that transferred genes may carry cis-regulatory elements encoded on the fragment of DNA that moves between species, facilitating their expression in the new genomic context. Evolutionary novelty may also increase the likelihood that selection retains a transferred gene. However, only a significant difference in expression level, not sequence divergence, between donor and recipient orthologs is associated with successful lateral gene transfer. Overall, our results show that most transferred genes degrade over time. However, those capable of regulating their own expression are more likely to persist and contribute to long-term evolutionary innovation. <h4>Significance Statement</h4>  Lateral gene transfer (LGT) can introduce novel traits into plant genomes, yet most transferred genes are only transient residents and are degenerating, with reduced expression, truncation, and elevated DNA methylation. However, a minority persist and are more likely to resemble their donor counterparts in expression, suggesting co-transfer of cis-regulatory elements. These findings indicate that regulatory compatibility is key to their long-term survival.\n\nRegulatory features determine the evolutionary fate of laterally acquired genes in plants", "token_count": 461, "char_count": 2348, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:10.597094", "source": {"split": "train_shard_00001", "doc_id": 620}, "chunk_id": "train_shard_00001_620_0", "global_id": 6534}
{"text": "The environmental bacterium <i>Klebsiella oxytoca</i> displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, <i>K. oxytoca</i> previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the <i>til</i> gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.\n\nCore genome multilocus sequence typing (cgMLST) applicable to the monophyletic <i>Klebsiella oxytoca</i> species complex.", "token_count": 446, "char_count": 1952, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:11.207133", "source": {"split": "train_shard_00001", "doc_id": 621}, "chunk_id": "train_shard_00001_621_0", "global_id": 6535}
{"text": "Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits but remain less explored compared to mRNA and classical phenotypes. This study systematically analyzed brain proteomes in a rat family using tandem mass tag (TMT)-based quantitative mass spectrometry. We quantified 8,119 proteins across two parental strains (SHR/Olalpcv and BN-Lx/Cub) and 29 HXB/BXH recombinant inbred (RI) strains, identifying 597 proteins with differential expression and 464 proteins linked to <i>cis</i>-acting quantitative trait loci (pQTLs). Proteogenomics identified 95 variant peptides, and sex-specific analyses revealed both shared and distinct <i>cis</i>-pQTLs. We improved the ability to pinpoint candidate genes underlying pQTLs by utilizing the rat pangenome and explored the connections between pQTLs in rats and human disorders. Collectively, this study highlights the value of large proteo-genetic datasets in elucidating protein modulation in the brain and its links to complex central nervous system (CNS) traits.\n\nGenetic modulation of protein expression in rat brain.", "token_count": 293, "char_count": 1120, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:11.752076", "source": {"split": "train_shard_00001", "doc_id": 622}, "chunk_id": "train_shard_00001_622_0", "global_id": 6536}
{"text": "<i>Parvimonas micra</i> is a Gram-positive, anaerobic bacterium commonly found in the oral cavity, skin and gastrointestinal tract. While typically a harmless organism, it can cause infections in individuals with weakened immune systems, leading to conditions like periodontitis and deep-tissue abscesses. This study focuses on the comparative genomic analysis of <i>P. micra</i> to explore its evolutionary relationships, antimicrobial resistance profiles and functional diversity by assessing phylogenetic analyses, resistance genes, virulence factors, mobile genetic elements, carbohydrate-active enzymes and pan-genome analysis. Comparative genomic analysis of 11 <i>P. micra</i> strains reveals significant functional variations among the strains, indicating notable interspecies diversity. Phylogenetic and comparative genome analysis revealed that strain JM503A is taxonomically distinct from the <i>P. micra</i> species, with genome similarity ranging from 54% to 61%. The 16S rRNA sequence similarity of strain JM503A is 98.28%, indicating a distinct phylogenetic position. The average nucleotide identity value ranging from 91.32% to 91.7% and digital DNA-DNA hybridization values ranging from 43.00% to 44.00% of JM503A with other strains are below the cutoff values <95% and <70%, respectively, which confirms JM503A as a novel species. Based on its evolutionary relationships, strain JM503A is identified as a potential new species of <i>Parvimonas</i>, providing important evidence for its reclassification as a new species within the genus <i>Parvimonas</i>.", "token_count": 443, "char_count": 1573, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": {"genes": ["JM503A"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:12.356624", "source": {"split": "train_shard_00001", "doc_id": 623}, "chunk_id": "train_shard_00001_623_0", "global_id": 6537}
{"text": "Comparative genome analysis of human pathogen &lt;i&gt;Parvimonas micra&lt;/i&gt; revealed strain JM503A as potential novel species in the genus &lt;i&gt;Parvimonas&lt;/i&gt; and high intra-species functional diversity.", "token_count": 74, "char_count": 219, "word_count": 24, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": ["JM503A"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:12.750070", "source": {"split": "train_shard_00001", "doc_id": 623}, "chunk_id": "train_shard_00001_623_1", "global_id": 6538}
{"text": "<h4>ABSTRACT</h4>  Microbial inoculants that integrate plant growth promotion, pathogen suppression, and pollutant degradation are central to sustainable agriculture. Here, we report the genomic and phenotypic characterization of Lysinibacillus capsici BCSIR-Raj-01, an endophyte isolated from citrus leaves in Bangladesh. The 4.62 Mb genome encodes 4,699 coding sequences and displays an open pangenome with loci linked to stress adaptation, xenobiotic degradation, and secondary metabolite biosynthesis. Genome mining revealed complete pathways for indole-3-acetic acid (IAA) production, siderophore biosynthesis, and phosphate metabolism, alongside gene clusters for bacteriocins, lantibiotics, terpenes, and polyketides. Nitrogen cycling genes indicated diazotrophic growth potential and a truncated denitrification pathway. Phenotypic assays validated these predictions: L. capsici BCSIR-Raj-01 solubilized phosphate, produced IAA and siderophores, grew on hydrocarbons, and exhibited diazotrophic activity. Notably, the strain showed potent larvicidal activity against Culex and Anopheles larvae, suggesting ecological roles beyond plant association. Together, these results establish L. capsici BCSIR-Raj-01 as a multifunctional bacterium with potential applications in crop improvement, bioremediation, and biological vector control. <h4>IMPORTANCE</h4>  The challenges of modern agriculture and environmental sustainability demand microbial solutions that deliver multiple functions. Lysinibacillus species are increasingly recognized for such versatility, but their genomic basis remains poorly resolved. Our study provides the first genome-enabled framework for understanding multifunctionality in L. capsici ", "token_count": 451, "char_count": 1720, "word_count": 204, "semantic_coherence": 1, "information_density": 0.7892, "quality_score": 0.8946, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:13.380453", "source": {"split": "train_shard_00001", "doc_id": 624}, "chunk_id": "train_shard_00001_624_0", "global_id": 6539}
{"text": "By combining whole-genome sequencing with phenotypic validation, we show that BCSIR-Raj-01 harbors biosynthetic clusters, stress adaptation loci, and xenobiotic degradation genes while also expressing experimentally confirmed traits, including phosphate solubilization, IAA and siderophore production, nitrogen fixation, hydrocarbon utilization, and larvicidal activity. This integration of plant growth promotion, biocontrol potential, and pollutant degradation positions L. capsici BCSIR-Raj-01 as a next-generation bioinoculant. Beyond broadening the functional scope of Lysinibacillus , our findings highlight how genome-guided approaches can identify microbes with cross-sectoral applications in agriculture, bioremediation, and vector management.\n\nMetabolic Versatility of <i>Lysinibacillus capsici</i> BCSIR-Raj-01 Underpins Its Multifunctionality in Biocontrol, Bioremediation, and Plant Growth Promotion", "token_count": 249, "char_count": 912, "word_count": 102, "semantic_coherence": 1, "information_density": 0.8529, "quality_score": 0.9265, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:13.881963", "source": {"split": "train_shard_00001", "doc_id": 624}, "chunk_id": "train_shard_00001_624_1", "global_id": 6540}
{"text": "<i>Proteus mirabilis</i> is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, <i>P. mirabilis</i> may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of <i>P. mirabilis</i> genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 <i>Proteus</i> genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related <i>P. mirabilis</i> genomes, and pan-genome annotation to identify genes of interest not present in the model <i>P. mirabilis</i> strain HI4320. Within our cohort, <i>Proteus</i> is composed of 10 named species and 5 uncharacterized genomospecies. <i>P. mirabilis</i> can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The <i>P. mirabilis</i> pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain <i>P. mirabilis</i> HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome", "token_count": 524, "char_count": 1807, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6397, "quality_score": 0.8198, "entities": {"genes": ["HI4320"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:14.534213", "source": {"split": "train_shard_00001", "doc_id": 625}, "chunk_id": "train_shard_00001_625_0", "global_id": 6541}
{"text": "IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on <i>P. mirabilis</i>, but similar to other Gram-negative bacteria, <i>P. mirabilis</i> has a mosaic genome with a linkage between phylogenetic position and accessory genome content. <i>P. mirabilis</i> encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.\n\nUncharacterized and lineage-specific accessory genes within the <i>Proteus mirabilis</i> pan-genome landscape.", "token_count": 250, "char_count": 1028, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8417, "entities": {"genes": ["HI4320"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:15.003353", "source": {"split": "train_shard_00001", "doc_id": 625}, "chunk_id": "train_shard_00001_625_1", "global_id": 6542}
{"text": "<h4>Background</h4> Indian cattle known as desi cattle, renowned for their adaptability to harsh environments and diverse phenotypic traits, represent a valuable genetic resource. While reference genome assemblies have been instrumental in advancing cattle genomics, they often fail to capture the full spectrum of genetic variation present within diverse populations. To address this limitation, we aimed to construct a pangenome for desi cattle by identifying and characterizing Non-Reference Novel Sequences (NRNS). <h4>Findings</h4> We sequenced 68 desi cattle genomes representing seven distinct breeds, generating 48.35 billion short reads. A PanGenome Analysis (PanGA) pipeline was developed in Bash scripts to process these data to identify NRNS missing in the reference genome. A total of 13,065 NRNS with a cumulative length of ∼41 Mbp were identified that exhibited substantial variation across the population. These NRNS were found to be exclusive to Indian desi cattle, matching only 4.1% with the Chinese indicine pangenome. However, a significant proportion (∼40%) of NRNS displayed ancestral origins within the Bos genus. These sequences were enriched in genic regions, suggesting functional roles, and were associated with quantitative trait loci (QTLs), particularly for milk production. Compared to a single reference genome, the pangenome approach significantly enhanced read mapping accuracy, reduced spurious SNP calls, and facilitated the discovery of novel genetic variants. <h4>Conclusions</h4> This study has successfully established a within-species cattle pangenome specifically focused on desi cattle breeds from India. Our findings highlight the importance of pangenome based analyses for understanding the complex genetic architecture of desi cattle.\n\nConstructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing", "token_count": 416, "char_count": 1855, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:15.600517", "source": {"split": "train_shard_00001", "doc_id": 626}, "chunk_id": "train_shard_00001_626_0", "global_id": 6543}
{"text": "<h4>Background</h4>Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives.<h4>Results</h4>We perform pangenome analysis on 2371 Streptomyces genomes, including approximately 1200 complete assemblies. Employing a data-driven approach based on genome similarities, the Streptomyces genus was classified into 7 primary and 42 secondary Mash-clusters, forming the basis for comprehensive pangenome mining. A refined workflow for grouping biosynthetic gene clusters (BGCs) redefines their diversity across different Mash-clusters. This workflow also reassigns 2729 known BGC families to only 440 families, a reduction caused by inaccuracies in BGC boundary detections. When the genomic location of BGCs is included in the analysis, a conserved genomic structure, or synteny, among BGCs becomes apparent within species and Mash-clusters. This synteny suggests that vertical inheritance is a major factor in the diversification of BGCs.<h4>Conclusions</h4>Our analysis of a genomic dataset at a scale of thousands of genomes refines predictions of BGC diversity using Mash-clusters as a basis for pangenome analysis. The observed conservation in the order of BGCs' genomic locations shows that the BGCs are vertically inherited. The presented workflow and the in-depth analysis pave the way for large-scale pangenome investigations and enhance our understanding of the biosynthetic potential of the Streptomyces genus.\n\nPangenome mining of the Streptomyces genus redefines species' biosynthetic potential.", "token_count": 447, "char_count": 1870, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8108, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:16.209255", "source": {"split": "train_shard_00001", "doc_id": 627}, "chunk_id": "train_shard_00001_627_0", "global_id": 6544}
{"text": "<h4>Background</h4>Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador.<h4>Results</h4>Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected.<h4>Conclusion</h4>This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance", "token_count": 516, "char_count": 2030, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8164, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:16.844228", "source": {"split": "train_shard_00001", "doc_id": 628}, "chunk_id": "train_shard_00001_628_0", "global_id": 6545}
{"text": "In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.\n\nComparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador.", "token_count": 67, "char_count": 306, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:17.202034", "source": {"split": "train_shard_00001", "doc_id": 628}, "chunk_id": "train_shard_00001_628_1", "global_id": 6546}
{"text": "<h4>Background</h4>The high prevalence and rapid emergence of antibiotic resistance in high-risk <i>Klebsiella pneumoniae (KP)</i> ST147 clones is a global health concern and warrants molecular surveillance.<h4>Methods</h4>A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.<h4>Results</h4>The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the <i>bla</i><sub>OXA-232</sub> gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the <i>acrAB</i> efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn<i>6170</i>, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the <i>tnsB</i> gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire <i>KP</i> population in 1621.<h4>Conclusions</h4>Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of <i>K. pneumoniae</i>. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.\n\nUnravelling the Evolutionary Dynamics of High-Risk <i>Klebsiella pneumoniae</i> ST147 Clones: Insights from Comparative Pangenome Analysis.", "token_count": 498, "char_count": 1741, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6759, "quality_score": 0.838, "entities": {"genes": ["ST147"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:17.824246", "source": {"split": "train_shard_00001", "doc_id": 629}, "chunk_id": "train_shard_00001_629_0", "global_id": 6547}
{"text": "The objective of this work was to deliver a comprehensive genetic characterization of a collection of <i>E. coli</i> strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family <i>Enterobacteriaceae</i>, together with other intestinal pathogens, such as <i>Shigella</i> spp. and <i>Salmonella</i> spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the <i>E. coli</i> strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic <i>E. coli</i> strains is particularly alarming for cheese production in artisan dairies.\n\n&lt;i&gt;Escherichia coli&lt;/i&gt; Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS).", "token_count": 402, "char_count": 1566, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:18.417071", "source": {"split": "train_shard_00001", "doc_id": 630}, "chunk_id": "train_shard_00001_630_0", "global_id": 6548}
{"text": "<i>Proteus mirabilis</i>, a significant pathogenic bacterium within the Enterobacteriaceae family, is widely distributed across various natural environments. This study conducted a genomic comparison analysis of 1,267 strains of <i>P. mirabilis</i> using extensive genome data from public databases. The objective was to elucidate the pan-genomic structure of <i>P. mirabilis</i>, revealing the composition and distribution of core and accessory gene families among different strains. Additionally, an attempt was made to construct a core genome multilocus sequence typing scheme specific to this species in order to enhance the precision of describing genetic diversity and evolutionary relationships. Furthermore, the study delved into the mechanisms of resistance of <i>P. mirabilis</i> to carbapenems and quinolones. Our findings underscore significant challenges posed by <i>P. mirabilis</i> in terms of antibiotic resistance, with widespread resistance observed particularly against beta-lactams and an increasing trend in resistance to carbapenems and quinolones. These results highlight the severity of <i>P. mirabilis</i> as a pathogen and underscore its rapid evolution and adaptability in developing resistance. This study aims to deepen our understanding of the antibiotic resistance of <i>P. mirabilis</i>, providing important insights for the development of future antimicrobial drugs, promoting effective treatment and control of this pathogen, and mitigating its threat to human health.<h4>Importance</h4>The bacterium <i>Proteus mirabilis</i> is a common pathogenic bacterium that is known to cause a variety of human infections. The drug-resistant genes carried by <i>P. mirabilis</i> present a significant challenge to clinical treatment, particularly in regard to the organism's notable resistance to commonly used beta-lactam and quinolone drugs. Furthermore, the prevalence of the urease gene cluster of <i>P. mirabilis</i> at the urease gene level may be associated with the formation of kidney stones. The objective of the study is to analyze the bacterium's drug resistance, urease gene clusters, and gene distribution in genomes in order to facilitate the development of antimicrobial drugs and improve the treatment and control of <i>P", "token_count": 530, "char_count": 2262, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5469, "quality_score": 0.7735, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:19.052572", "source": {"split": "train_shard_00001", "doc_id": 631}, "chunk_id": "train_shard_00001_631_0", "global_id": 6549}
{"text": "mirabilis</i> infections.\n\nGenomic insights on cgMLST markers, drug resistance, and urease cluster of <i>Proteus mirabilis</i> strains.", "token_count": 45, "char_count": 135, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:19.403614", "source": {"split": "train_shard_00001", "doc_id": 631}, "chunk_id": "train_shard_00001_631_1", "global_id": 6550}
{"text": "The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.\n\nUPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.", "token_count": 299, "char_count": 1247, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7349, "quality_score": 0.8675, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:19.941716", "source": {"split": "train_shard_00001", "doc_id": 632}, "chunk_id": "train_shard_00001_632_0", "global_id": 6551}
{"text": "<h4>Background</h4>Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequencing (SRS) samples. With the extensive growth in publicly available SRS datasets, it is now possible to calculate accurate population allele frequencies of SVs. However, reprocessing hundreds of terabytes of raw SRS data to genotype new variants is impractical for population-scale studies, a computational challenge known as the N+1 problem (i.e., the challenge of re-genotyping an entire cohort for one additional variant). Overcoming this computational bottleneck is essential for analyzing new SVs from the growing number of pangenomes, public genomic databases, and pathogenic variant discovery studies.<h4>Results</h4>We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem. Applied to a human dataset, the workflow begins by preprocessing 4.2k short-read samples of a total of 183 TB raw data to create an 867-GB Counting Colored de Bruijn Graph (CCDG). The Great Genotyper uses this CCDG to genotype a list of phased or unphased variants, leveraging the CCDG population information to increase both precision and recall. The Great Genotyper offers the same accuracy as the state-of-the-art genotypers while achieving unprecedented performance. It took about 100 hours to genotype 4.5M variants across the 4.2k samples and calculate their population allele frequencies using 1 server with 32 cores and 145 GB of memory. The Great Genotyper opens the door to new ways to study SVs. For example, using the premade index, we demonstrate the Great Genotyper's application in finding pathogenic variants by calculating accurate allele frequency for novel SVs. Also, we used it to create a 4k reference panel by genotyping variants from the Human Pangenome Reference Consortium (HPRC). The new reference panel allows for SV imputation from genotyping microarrays", "token_count": 516, "char_count": 2023, "word_count": 294, "semantic_coherence": 1, "information_density": 0.5986, "quality_score": 0.7993, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:20.566605", "source": {"split": "train_shard_00001", "doc_id": 633}, "chunk_id": "train_shard_00001_633_0", "global_id": 6552}
{"text": "Moreover, we genotype the human GWAS Catalog and merge its variants with the 4k reference panel. We show 6,253 events of high linkage between the HPRC's SVs and nearby GWAS single-nucleotide polymorphisms, which can help in interpreting the effect of these SVs on gene functions. This analysis uncovers the detailed haplotype structure of the human fibrinogen locus and revives the pathogenic association of a 28-bp insertion in the FGA gene with thromboembolic disorders.<h4>Conclusion</h4>The Great Genotyper solves the N+1 problem for population-scale genotyping of small and structural variants, offering both high accuracy and efficiency. Its ability to rapidly re-genotype large cohorts paves the road for several new studies of SVs.\n\nThe Great Genotyper: a graph-based method for population genotyping of small and structural variants.", "token_count": 228, "char_count": 842, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:21.015789", "source": {"split": "train_shard_00001", "doc_id": 633}, "chunk_id": "train_shard_00001_633_1", "global_id": 6553}
{"text": "<h4>Motivation</h4>Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data.<h4>Results</h4>We show that the combination of a well-known anchor-based method with the technique of prefix-free parsing yields an approach that is able to generate multiple alignments on a pangenomic scale, provided that large-scale structural variants are rare. Furthermore, experiments with real world data show that our software tool PANgenomic Anchor-based Multiple Alignment significantly outperforms current state-of-the art programs.<h4>Availability and implementation</h4>Source code is available at: https://gitlab.com/qwerzuiop/panama, archived at swh:1:dir:e90c9f664995acca9063245cabdd97549cf39694.\n\nGenerating multiple alignments on a pangenomic scale.", "token_count": 296, "char_count": 1174, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:21.555615", "source": {"split": "train_shard_00001", "doc_id": 634}, "chunk_id": "train_shard_00001_634_0", "global_id": 6554}
{"text": "<h4>ABSTRACT</h4> Bradyrhizobium is known for its ability to fix atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight putative natural variants of B. japonicum SEMIA 586 (=CNPSo 17) or B. diazoefficiens SEMIA 566 (=CNPSo 10), previously used as commercial inoculants for soybean crops in Brazil. We aimed to detect genetic variations that might be related to biological nitrogen fixation, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains and used for comparative genomic analyses. The core genome phylogeny revealed that strains of each group are closely related, confirmed by high average nucleotide identity (ANI) values. However, variants accumulated divergences resulting from horizontal gene transfer (HGT), genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, probably due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed in light of the observed differences in their nitrogen fixation capacity, competitiveness for nodule occupancy, and environmental adaptation. <h4>SIGNIFICANCE</h4> The two main reference strains for soybean inoculation in Brazil, B. japonicum CPAC 15 (=SEMIA 5079) and B. diazoefficiens CPAC 7 (=SEMIA 5080), have been considered highly competitive and highly efficient in nitrogen fixation, respectively. In this study, we obtained and analyzed the genomes of the parental and variant strains. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation", "token_count": 531, "char_count": 2082, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7912, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:22.185827", "source": {"split": "train_shard_00001", "doc_id": 635}, "chunk_id": "train_shard_00001_635_0", "global_id": 6555}
{"text": "Our analysis contributes to new insights into evolution of Bradyrhizobium , and some of the identified differences may be applied as genetic markers to assist strain selection programs.\n\nComparative genomic analysis of<i>Bradyrhizobium</i>strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions", "token_count": 87, "char_count": 382, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8542, "quality_score": 0.9271, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:22.546472", "source": {"split": "train_shard_00001", "doc_id": 635}, "chunk_id": "train_shard_00001_635_1", "global_id": 6556}
{"text": "<h4>Background</h4> A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers, that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multi-copy gene families (recognizable by synteny conservation) and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. <h4>Results</h4> Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, which allows for robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. <h4>Conclusions</h4> Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.\n\nComparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses", "token_count": 438, "char_count": 2034, "word_count": 260, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:23.152485", "source": {"split": "train_shard_00001", "doc_id": 636}, "chunk_id": "train_shard_00001_636_0", "global_id": 6557}
{"text": "BACKGROUND AND OBJECTIVES: In this study, Kluyveromyces marxianus with ability to produce β‐glucosidase was used to preferment wheat bran (WB) and release a mixture of natural enzymes for improving dough performance and bread quality. Five different enzyme activities were analyzed. The effect of the prefermented WB with enzyme mixture on stickiness and microstructure of dough, ferulic acid release in bread, and molecular weight distribution of arabinoxylan were evaluated using Texture Analyzer, scanning electron microscopy (SEM), HPLC, and high‐performance gel filtration chromatography (HPGFC). FINDINGS: Kluyveromyces marxianus exhibited abundant extracellular β‐glucosidase activity (up to 6.98 U/g). The main enzymes released in prefermented bran were endoglucanase and exoglucanase, β‐glucosidase, xylanase, and ferulate esterases. These enzymes were active during bread making (only prefermented bran added as improver or combined with xylanase) and affected solubility and molecular weight distribution of dietary fiber, which resulted in positive improvement of dough performance, release of phenolic acid, and overall quality of the breads. The changes observed were attributed to the extracellular enzymes from K. marxianus and endogenous enzymes activated during prefermentation, thus enhancing the WB functionality in bread. CONCLUSIONS: Wheat bran bioprocessing using high enzyme producing yeasts increases functional application of wheat bran in baked products. SIGNIFICANCE AND NOVELTY: This study added new knowledge for developing a natural enzyme‐based improver for bran‐enriched baked products in the food industry.\n\nUse of Kluyveromyces marxianus prefermented wheat bran as a source of enzyme mixture to improve dough performance and bread biochemical properties", "token_count": 467, "char_count": 1788, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6017, "quality_score": 0.8008, "entities": {"genes": [], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:23.773921", "source": {"split": "train_shard_00001", "doc_id": 637}, "chunk_id": "train_shard_00001_637_0", "global_id": 6558}
{"text": "Seven strains of selected probiotic bacteria were separately combined with Kluyveromyces marxianus LAF4 to ferment 12% reconstituted skim milk (RSM) at 37 °C for 0–12 h. The growth characteristics of the probiotic strains and K. marxianus, pH levels, proteolytic activity and angiotensin‐converting enzyme inhibitory (ACE‐I) activity of the fermented RSM were measured. The highest ACE‐I activity of 60% was for K. marxianus at 37 °C for 12 h (P < 0.005) when compared to K. marxianus in combination with the probiotic bacterial strains.\n\nEffects of fermented skim milk drink by Kluyveromyces marxianus LAF4 co‐cultured with lactic acid bacteria to release angiotensin‐converting enzyme inhibitory activities", "token_count": 233, "char_count": 708, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": {"genes": ["LAF4"], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces"], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:24.235583", "source": {"split": "train_shard_00001", "doc_id": 638}, "chunk_id": "train_shard_00001_638_0", "global_id": 6559}
{"text": "Nowadays, biofuels, especially bioethanol, are becoming increasingly popular as an alternative to fossil fuels. Zymomonas mobilis is a desirable species for bioethanol production due to its unique characteristics, such as low biomass production and high-rate glucose metabolism. However, several factors can interfere with the fermentation process and hinder microbial activity, including lignocellulosic hydrolysate inhibitors, high temperatures, an osmotic environment, and high ethanol concentration. Overcoming these limitations is critical for effective bioethanol production. In this review, the stress response mechanisms of Z. mobilis are discussed in comparison to other ethanol-producing microbes. The mechanism of stress response is divided into physiological (changes in growth, metabolism, intracellular components, and cell membrane structures) and molecular (up and down-regulation of specific genes and elements of the regulatory system and their role in expression of specific proteins and control of metabolic fluxes) changes. Systemic metabolic engineering approaches, such as gene manipulation, overexpression, and silencing, are successful methods for building new metabolic pathways. Therefore, this review discusses systems metabolic engineering in conjunction with systems biology and synthetic biology as an important method for developing new strains with an effective response mechanism to fermentation stresses during bioethanol production. Overall, understanding the stress response mechanisms of Z. mobilis can lead to more efficient and effective bioethanol production.\n\nComprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering.", "token_count": 382, "char_count": 1793, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism", "fermentation"], "organisms": [], "conditions": ["ph", "temperature", "osmotic"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:24.823556", "source": {"split": "train_shard_00001", "doc_id": 639}, "chunk_id": "train_shard_00001_639_0", "global_id": 6560}
{"text": "<h4>Background</h4> After introduction of pneumococcal conjugate vaccines (PCVs), serotype replacement occurred in the population of Streptococcus pneumoniae. Predicting which pneumococcal clones and serotypes will become more common in carriage after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. We sought to use invasive disease data to assess how well negative frequency-dependent selection (NFDS) models could explain pneumococcal carriage population evolution in the post-PCV13 epoch by weighting invasive data to approximate strain proportions in the carriage population. <h4>Methods</h4> Invasive pneumococcal isolates were collected and sequenced during 1998–2018 by the Active Bacterial Core surveillance (ABCs) from the Centers for Disease Control and Prevention (CDC). To predict the post-PCV13 population dynamics in the carriage population using a NFDS model, all genomic data were processed under a bioinformatic pipeline of assembly, annotation, and pangenome analysis to define genetically similar sequence clusters (i.e., strains) and a set of accessory genes present in 5% to 95% of the isolates. The NFDS model predicted the strain proportion by calculating the post-vaccine strain composition in the weighted invasive disease population that would best match pre-vaccine accessory gene frequencies. To overcome the biases of invasive disease data, serotype-specific inverse-invasiveness weights were defined as the ratio of the proportion of the serotype in the carriage data to the proportion in the invasive data, using data from 1998–2001 in the United States, before conjugate vaccine introduction. The weights were applied to adjust both the observed strain proportion and the accessory gene frequencies. <h4>Results</h4> Inverse-invasiveness weighting increased the correlation of accessory gene frequencies between invasive and carriage data with reduced residuals in linear or logit scale for pre-vaccine, post-PCV7, and post-PCV13. Similarly, weighting increased the correlation of accessory gene frequencies between different time periods in the invasive data", "token_count": 510, "char_count": 2182, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7797, "entities": {"genes": ["PCV13", "PCV7"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:25.474890", "source": {"split": "train_shard_00001", "doc_id": 640}, "chunk_id": "train_shard_00001_640_0", "global_id": 6561}
{"text": "By weighting the invasive data, we were able to use the NFDS model to predict strain proportions in the carriage population in the post-PCV13 epoch, with the adjusted R-squared between predicted and observed strain proportions increasing from 0.176 to 0.544 after weighting. <h4>Conclusions</h4> The weighting system adjusted the invasive disease surveillance data to better represent the carriage population of S. pneumoniae . The NFDS mechanism predicted the strain proportions in the projected carriage population as estimated from the weighted invasive disease frequencies in the post-PCV13 epoch. Our methods enrich the value of genomic sequences from invasive disease surveillance, which is readily available, easy to collect, and of direct interest to public health. <h4>IMPORTANCE</h4> Streptococcus pneumoniae , a common colonizer in the human nasopharynx, can cause invasive diseases including pneumonia, bacteremia, and meningitis mostly in children under 5 years or older adults. The PCV7 was introduced in 2000 in the United States within the pediatric population to prevent disease and reduce deaths, followed by PCV13 in 2010, PCV15 in 2022, and PCV20 in 2023. After the removal of vaccine serotypes, the prevalence of carriage remained stable as the vacated pediatric ecological niche was filled with certain non-vaccine serotypes. Predicting which pneumococcal clones, and which serotypes, will be most successful in colonization after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. While carriage data, which are collected from the pneumococcal population that is competing to colonize and transmit, are most directly relevant to evolutionary studies, invasive disease data are often more plentiful. Previously, evolutionary models based on negative frequency-dependent selection (NFDS) on the accessory genome were shown to predict which non-vaccine strains and serotypes were most successful in colonization following the introduction of PCV7", "token_count": 488, "char_count": 2053, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5773, "quality_score": 0.7887, "entities": {"genes": ["PCV13", "PCV20", "PCV15", "PCV7"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:26.127162", "source": {"split": "train_shard_00001", "doc_id": 640}, "chunk_id": "train_shard_00001_640_1", "global_id": 6562}
{"text": "Here, we show that an inverse-invasiveness weighting system applied to invasive disease surveillance data allows the NFDS model to predict strain proportions in the projected carriage population in the post-PCV13/pre-PCV15 and -PCV20 epoch. The significance of our research lies in using a sample of invasive disease surveillance data to extend the use of NFDS as an evolutionary mechanism to predict post-PCV13 population dynamics. This has shown that we can correct for biased sampling that arises from differences in virulence and can enrich the value of genomic data from disease surveillance and advances our understanding of how NFDS impacts carriage population dynamics after both PCV7 and PCV13 vaccination.\n\nPrediction of post-PCV13 pneumococcal evolution using invasive disease data enhanced by inverse-invasiveness weighting", "token_count": 190, "char_count": 835, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": {"genes": ["PCV13", "PCV20", "PCV15", "PCV7"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:26.572194", "source": {"split": "train_shard_00001", "doc_id": 640}, "chunk_id": "train_shard_00001_640_2", "global_id": 6563}
{"text": "Kluyveromyces marxianus is a multifaceted yeast used in the dairy, biotechnological, and probiotic industries, and has been implicated in the spoilage of dairy products. Currently, K. marxianus detection involves laborious and time-consuming culture methods. To develop a rapid and reliable detection method for K. marxianus in pure cultures and dairy products, we designed a novel real-time PCR primer/probe set, KM55, which targets the internal transcribed spacer (ITS) rRNA gene. In the inclusivity and exclusivity tests, 11 K. marxianus strains tested positive, while 28 closely related microorganisms tested negative; this confirmed 100% sensitivity and specificity of the assay. Further, the KM55 set enabled a linear K. marxianus detection in the range of 100–105 colony-forming units (CFU) per reaction in phosphate-buffered saline, 10% skim milk, and commercial yogurts, with no cross-reactivity with microorganisms of kefir origin. The enumeration of K. marxianus in kefir revealed 5.1 to 6.9 logCFU ml−1 of kefir, depending on the fermentation time, temperature, and grain-milk ratio. K. marxianus was successfully detected in artificially contaminated yogurt samples within 2 h. These results suggest that this method could be an effective and sensitive presumptive screening tool for detecting and enumerating K. marxianus in dairy products.\n\nDevelopment of a rapid and reliable TaqMan probe-based real-time PCR assay for the detection and enumeration of the multifaceted yeast Kluyveromyces marxianus in dairy products", "token_count": 432, "char_count": 1532, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": {"genes": ["KM55"], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["ph", "temperature"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:27.172676", "source": {"split": "train_shard_00001", "doc_id": 641}, "chunk_id": "train_shard_00001_641_0", "global_id": 6564}
{"text": "<h4>Background</h4>The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge.<h4>Results</h4>To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation.<h4>Conclusions</h4>The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .\n\nCamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter.", "token_count": 360, "char_count": 1622, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:27.726664", "source": {"split": "train_shard_00001", "doc_id": 642}, "chunk_id": "train_shard_00001_642_0", "global_id": 6565}
{"text": "Tuberculosis is a major public health threat demanding more than one million lives every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 of which are core genes. However, due to 99,694 interruptions in 2,447 coding genes, only 1,651 may be translated in all samples, which dramatically reduces the number of active core genes. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structure variations, mostly small indels. We further describe differential evolutionary patterns of genes under the influences of selective pressure, population structure and background selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations primarily occur in 1,313 genes. Genes located in the cell wall and membrane region are under the strongest selective pressure, while biological processes including regulation of transcription, translation and regulation of growth are under strongest background selection in MTB. The metabolism of fatty acids may be an outstanding example of evolutionary adaption for MTB under current selective pressure. This study provides a comprehensive view on the genetic diversity and evolution patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.\n\nUnderstanding the epidemiology and pathogenesis of<i>Mycobacterium tuberculosis</i>with non-redundant pangenome and population genetics", "token_count": 424, "char_count": 1840, "word_count": 261, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["acid"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:28.325974", "source": {"split": "train_shard_00001", "doc_id": 643}, "chunk_id": "train_shard_00001_643_0", "global_id": 6566}
{"text": "In this study, a high-throughput sequencing technique was used to analyze bacterial and fungal diversity of two traditional Tibetan kefir grains from Linzhi (K1) and Naqu (K2) regions. Comparative bioinformatic analyses indicated that <i>Lactobacillus kefiranofaciens</i>, <i>L. kefiri</i> and <i>Kluyveromyces marxianus</i> were the main dominant strains in K1 and K2. In order to research the relationship of the growth of kefir grains, the biofilm and the extracellular polysaccharides (EPS) produced by microorganisms, the proliferation rate of kefir grains, the yield and chemical structure of EPS and the optimal days for biofilm formation were determined. The results showed that the growth rate, the yield of EPS and the biofilm formation ability of K1 were higher than K2, and the optimal day of their biofilm formation was the same in 10th day. Additionally, the live cells, dead cells and EPS in biofilm formation of K1 and K2 were observed by fluorescence microscope to clarify the formation process of kefir grains. To determine the influence of microbial interactions on biofilm and the formation of kefir grains, the essential role of microbial quorum sensing needs further attention.\n\nThe Microbial Diversity and Biofilm-Forming Characteristic of Two Traditional Tibetan Kefir Grains.", "token_count": 346, "char_count": 1300, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5464, "quality_score": 0.7732, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:28.880598", "source": {"split": "train_shard_00001", "doc_id": 644}, "chunk_id": "train_shard_00001_644_0", "global_id": 6567}
{"text": "<h4>ABSTRACT</h4>  A variety of marine invertebrates are known to form associations with chemosynthetic bacteria, but to the best of our knowledge this has not been documented in fishes. Here, we apply genome-resolved metagenomics to the hamlets ( Hypoplectrus spp), a model system for the study of speciation in the sea. The analysis of 304 gill samples from 12 hamlet species collected at six locations over 13 years revealed a stark contrast between the gill microbiota and ambient water microbial communities. One novel lineage in the Burkholderiaceae-B family was particularly prevalent across host species, sampling locations and years. Its genome encoded highly complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. Its pangenome revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), paralleling the phylogenomic pattern observed in the hamlet radiation. Our survey also identified genomes of multiple novel gill-associated lineages related to known fish gill pathogens, fish gut microbes and free-living seawater taxa. These lineages harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. Overall, our findings suggest complex host-microbe and microbe-microbe eco-evolutionary interactions that may influence fish physiology, homeostasis and immune response.\n\nProteobacteria with chemosynthetic potential are highly enriched in the gills of <i>Hypoplectrus</i> reef fishes", "token_count": 385, "char_count": 1589, "word_count": 214, "semantic_coherence": 1, "information_density": 0.743, "quality_score": 0.8715, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:29.474113", "source": {"split": "train_shard_00001", "doc_id": 645}, "chunk_id": "train_shard_00001_645_0", "global_id": 6568}
{"text": "Milk beer is a new type of milk beverage produced by two‐step fermentation of lactic acid bacteria and yeast and created first in China. Yeast is the key strain of milk beer fermentation, which determines the flavor and quality of milk beer. In this study, the preparation process of high‐quality yeast strain MJ1 active freeze‐dried powder suitable for milk beer fermentation was optimized. Results showed that the optimal freeze‐dried protective agent was used: sucrose 11.27%, mannitol 4.88%, maltodextrin 15.43%, skimmed milk powder 7.82%, and applying the optimal freeze‐drying conditions: rotation speed 6,000 rpm, centrifugation time 15 min, the mixing ratio of centrifugal bacterial sludge and the protective agent is 1:1.5, the mixing equilibrium time is 30 min, the cell survival rate of strain MJ1 can reach 90.21% ± 1.04%. It laid the foundation for the preparation of active freeze‐dried yeast powder and the industrial production of milk beer. NOVELTY IMPACT STATEMENT: (1) The formulation and conditions of the freeze‐dried protectant of Kluyveromyces marxianus yeast strain MJ1 were optimized to improve the cell survival rate of the freeze‐dried yeast powder, (2) the optimal storage conditions of the freeze‐dried yeast powder of strain MJ1 were screened to provide theoretical reference for the long‐term storage of freeze‐dried yeast powder, and (3) the fermentation performance of the freeze‐dried yeast powder of strain MJ1 was verified, which provided a reliable basis for the industrial production of milk beer.\n\nScreening of the freeze‐drying protective agent for high‐quality milk beer yeast (Kluyveromyces marxianus) and optimization of freeze‐drying process conditions", "token_count": 448, "char_count": 1696, "word_count": 252, "semantic_coherence": 1, "information_density": 0.4802, "quality_score": 0.7401, "entities": {"genes": ["MJ1"], "proteins": [], "pathways": ["fermentation"], "organisms": ["marxianus", "kluyveromyces", "yeast"], "conditions": ["acid"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:30.081376", "source": {"split": "train_shard_00001", "doc_id": 646}, "chunk_id": "train_shard_00001_646_0", "global_id": 6569}
{"text": "Probiotics are health-beneficial microorganisms with mainly immunomodulatory and anti-inflammatory properties. <i>Lactobacillus delbrueckii</i> species is a common bacteria used in the dairy industry, and their benefits to hosting health have been reported. This study analyzed the core genome of nine strains of <i>L. delbrueckii</i> species with documented probiotic properties, focusing on genes related to their host health benefits. For this, a combined methodology including several software and databases (BPGA, SPAAN, BAGEL4, BioCyc, KEEG, and InterSPPI) was used to predict the most important characteristics related to <i>L. delbrueckii</i> strains probiose. Comparative genomics analyses revealed that <i>L. delbrueckii</i> probiotic strains shared essential genes related to acid and bile stress response and antimicrobial activity. Other standard features shared by these strains are surface layer proteins and extracellular proteins-encoding genes, with high adhesion profiles that interacted with human proteins of the inflammatory signaling pathways (TLR2/4-MAPK, TLR2/4-NF-κB, and NOD-like receptors). Among these, the PrtB serine protease appears to be a strong candidate responsible for the anti-inflammatory properties reported for these strains. Furthermore, genes with high proteolytic and metabolic activity able to produce beneficial metabolites, such as acetate, bioactive peptides, and B-complex vitamins were also identified. These findings suggest that these proteins can be essential in biological mechanisms related to probiotics' beneficial effects of these strains in the host.\n\nGenomic Characterization of <i>Lactobacillus delbrueckii</i> Strains with Probiotics Properties.", "token_count": 442, "char_count": 1707, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": {"genes": ["TLR2", "BAGEL4"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["acid", "bile"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:30.690193", "source": {"split": "train_shard_00001", "doc_id": 647}, "chunk_id": "train_shard_00001_647_0", "global_id": 6570}
{"text": "Language Models (LM) have been extensively utilized for learning DNA sequence patterns and generating synthetic sequences. In this paper, we present a novel approach for the generation of synthetic DNA data using pangenomes in combination with LM. We introduce three innovative pangenome-based tokenization schemes, including two that can decouple from private data, while enhance long DNA sequence generation. Our experimental results demonstrate the superiority of pangenome-based tokenization over classical methods in generating high-utility synthetic DNA sequences, highlighting a promising direction for the public sharing of genomic datasets.\n\nPangenome-Informed Language Models for Synthetic Genome Sequence Generation", "token_count": 140, "char_count": 726, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:31.119589", "source": {"split": "train_shard_00001", "doc_id": 648}, "chunk_id": "train_shard_00001_648_0", "global_id": 6571}
{"text": "Multipartite genomes are thought to confer evolutionary advantages to bacteria by providing greater metabolic flexibility in fluctuating environments and enabling rapid adaptation to new ecological niches and stress conditions. This genome architecture is commonly found in plant symbionts, including nitrogen-fixing rhizobia, such as <i>Rhizobium leguminosarum</i> bv. <i>trifolii</i> TA1 (RtTA1), whose genome comprises a chromosome and four extrachromosomal replicons (ECRs). In this study, the transcriptomic responses of RtTA1 to partial nutrient limitation and low acidic pH were analyzed using high-throughput RNA sequencing. RtTA1 growth under these conditions resulted in the differential expression of 1035 to 1700 genes (DEGs), which were assigned to functional categories primarily related to amino acid and carbohydrate metabolism, ribosome and cell envelope biogenesis, signal transduction, and transcription. These results highlight the complexity of the bacterial response to stress. Notably, the distribution of DEGs among the replicons indicated that ECRs played a significant role in the stress response. The transcriptomic data align with the <i>Rhizobium</i> pangenome analysis, which revealed an over-representation of functional categories related to transport, metabolism, and regulatory functions on ECRs. These findings confirm that ECRs contribute substantially to the ability of rhizobia to adapt to challenging environmental conditions.\n\nTranscriptomic Response of <i>Rhizobium leguminosarum</i> to Acidic Stress and Nutrient Limitation Is Versatile and Substantially Influenced by Extrachromosomal Gene Pool.", "token_count": 410, "char_count": 1638, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6714, "quality_score": 0.8357, "entities": {"genes": ["TA1"], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:31.718456", "source": {"split": "train_shard_00001", "doc_id": 649}, "chunk_id": "train_shard_00001_649_0", "global_id": 6572}
{"text": "As Arctic soil ecosystems warm due to climate change, enhanced microbial activity is projected to increase the rate of soil organic matter degradation. Delineating the diversity and activity of Arctic tundra microbial communities active in decomposition is thus of keen interest. Here, we describe novel cold-adapted bacteria in the genus <i>Mucilaginibacter</i> (<i>Bacteroidota</i>) isolated from Artic tundra soils in Finland. These isolates are aerobic chemoorganotrophs and appear well adapted to the low-temperature environment, where they are also exposed to desiccation and a wide regime of annual temperature variation. Initial 16S ribosomal RNA (rRNA)-based phylogenetic analysis suggested that five isolated strains represent new species of the genus <i>Mucilaginibacter</i>, confirmed by whole genome-based phylogenomic and average nucleotide identity. Five novel species are described: <i>Mucilaginibacter geliditolerans</i> sp. nov., <i>Mucilaginibacter tundrae</i> sp. nov., <i>Mucilaginibacter empetricola</i> sp. nov., <i>Mucilaginibacter saanensis</i> sp. nov., and <i>Mucilaginibacter cryoferens</i> sp. nov. Genome and phenotype analysis showed their potential in complex carbon degradation, nitrogen assimilation, polyphenol degradation, and adaptation to their tundra heath habitat. A pangenome analysis of the newly identified species alongside known members of the <i>Mucilaginibacter</i> genus sourced from various environments revealed the distinctive characteristics of the tundra strains. These strains possess unique genes related to energy production, nitrogen uptake, adaptation, and the synthesis of secondary metabolites that aid in their growth, potentially accounting for their prevalence in tundra soil. By uncovering novel species and strains within the <i>Mucilaginibacter</i>, we enhance our understanding of this genus and elucidate how environmental fluctuations shape the microbial functionality and interactions in Arctic tundra ecosystems.", "token_count": 519, "char_count": 1983, "word_count": 252, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph", "temperature"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:32.350025", "source": {"split": "train_shard_00001", "doc_id": 650}, "chunk_id": "train_shard_00001_650_0", "global_id": 6573}
{"text": "Genome analysis reveals diverse novel psychrotolerant &lt;i&gt;Mucilaginibacter&lt;/i&gt; species in Arctic tundra soils.", "token_count": 41, "char_count": 121, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:32.697712", "source": {"split": "train_shard_00001", "doc_id": 650}, "chunk_id": "train_shard_00001_650_1", "global_id": 6574}
{"text": "The enteric, pathogenic spirochaete <i>Brachyspira pilosicoli</i> colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several <i>in silico</i> techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus <i>Brachyspira</i>. Our study revealed that an additional isolate that was unable to be species typed against any other <i>Brachyspira</i> lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the <i>B. pilosicoli</i> as random mutation (<i>r</i>/<i>m</i>=1.02). Comparative genomics has informed <i>Brachyspira</i> diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.\n\nEvidence of homologous recombination as a driver of diversity in <i>Brachyspira pilosicoli</i>.", "token_count": 390, "char_count": 1488, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6768, "quality_score": 0.8384, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:33.606242", "source": {"split": "train_shard_00001", "doc_id": 651}, "chunk_id": "train_shard_00001_651_0", "global_id": 6575}
{"text": "<h4>Background</h4>Although Escherichia coli (E. coli) is the most studied prokaryote organism in the history of life sciences, many molecular mechanisms and gene functions encoded in its genome remain to be discovered. This work aims at quantifying the illumination of the E. coli gene function space by the scientific literature and how close we are towards the goal of a complete list of E. coli gene functions.<h4>Results</h4>The scientific literature about E. coli protein-coding genes has been mapped onto the genome via the mentioning of names for genomic regions in scientific articles both for the case of the strain K-12 MG1655 as well as for the 95%-threshold softcore genome of 1324 E. coli strains with known complete genome. The article match was quantified with the ratio of a given gene name's occurrence to the mentioning of any gene names in the paper. The various genome regions have an extremely uneven literature coverage. A group of elite genes with ≥ 100 full publication equivalents (FPEs, FPE = 1 is an idealized publication devoted to just a single gene) attracts the lion share of the papers. For K-12, ~ 65% of the literature covers just 342 elite genes; for the softcore genome, ~ 68% of the FPEs is about only 342 elite gene families (GFs). We also find that most genes/GFs have at least one mentioning in a dedicated scientific article (with the exception of at least 137 protein-coding transcripts for K-12 and 26 GFs from the softcore genome). Whereas the literature growth rates were highest for uncharacterized or understudied genes until 2005-2010 compared with other groups of genes, they became negative thereafter. At the same time, literature for anyhow well-studied genes started to grow explosively with threshold T10 (≥ 10 FPEs). Typically, a body of ~ 20 actual articles generated over ~ 15 years of research effort was necessary to reach T10", "token_count": 515, "char_count": 1886, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7977, "entities": {"genes": ["MG1655"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:34.240420", "source": {"split": "train_shard_00001", "doc_id": 652}, "chunk_id": "train_shard_00001_652_0", "global_id": 6576}
{"text": "Lineage-specific co-occurrence analysis of genes belonging to the accessory genome of E. coli together with genomic co-localization and sequence-analytic exploration hints previously completely uncharacterized genes yahV and yddL being associated with osmotic stress response/motility mechanisms.<h4>Conclusion</h4>If the numbers of scientific articles about uncharacterized and understudied genes remain at least at present levels, full gene function lists for the strain K-12 MG1655 and the E. coli softcore genome are in reach within the next 25-30 years. Once the literature body for a gene crosses 10 FPEs, most of the critical fundamental research risk appears overcome and steady incremental research becomes possible.\n\nAbout the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature.", "token_count": 202, "char_count": 853, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7179, "quality_score": 0.859, "entities": {"genes": ["MG1655"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["osmotic"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:34.685820", "source": {"split": "train_shard_00001", "doc_id": 652}, "chunk_id": "train_shard_00001_652_1", "global_id": 6577}
{"text": "Individuals of Pacific ancestry suffer some of the highest rates of health disparities yet remain vastly underrepresented in genomic research, including currently available linear and pangenome references. To begin addressing this, we developed the first Pacific ancestry pangenome reference using 23 individuals with diverse Pacific ancestry. We assembled 46 haploid genomes from these 23 individuals, resulting in highly accurate and contiguous genome assemblies with an average quality value of 55.0 and an average N50 of 40.7 Mb, marking the first de novo assembly of highly accurate Pacific ancestry genomes. We combined these assemblies to create a pangenome reference, which added 30.6 Mb of novel sequence missing from the Human Pangenome Reference Consortium (HPRC) reference. Mapping short reads to this pangenome reduced variant call errors and yielded more true-positive variants compared to the HPRC and T2T-CHM13 references. This Pacific ancestry pangenome reference serves as a resource to enhance genetic analyses for this underserved population.\n\nA Draft Pacific Ancestry Pangenome Reference", "token_count": 260, "char_count": 1108, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.827, "entities": {"genes": ["CHM13"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:35.213822", "source": {"split": "train_shard_00001", "doc_id": 653}, "chunk_id": "train_shard_00001_653_0", "global_id": 6578}
{"text": "Cytosine methylation, a crucial epigenetic modification, plays a vital role in genomic regulation. Leveraging the advancements in third-generation sequencing, we investigated the methylation patterns of non-reference insertions of human lymphoblastoid cell lines (LCLs), particularly polymorphic transposable elements (TEs). We validated the high concordance between long-read methylation calls and conventional whole genome bisulfite sequencing (WGBS) method. By characterizing thousands of polymorphic TE insertions genome-wide using long reads from the draft Human Pangenome Reference, we aimed to establish general rules of TE methylation by addressing three key questions: 1) what is the methylation profile of each insertion? 2) do newly inserted TEs adopt the methylation pattern of their genomic context? and 3) do new TE insertions affect the methylation of their flanking regions? While most non-TE insertions exhibit DNA methylation patterns consistent with their genomic context, TE insertions are generally highly methylated, exhibiting distinct, class-specific patterns, and with profound variation within TE bodies. A small percentage of Alu insertions are hypomethylated, particularly those inserted within hypomethylated CpG islands. By comparing DNA methylation of flanking regions of TE insertions between individuals with and without the TE insertions, we revealed that majority of TEs exhibited minimal impact on nearby regions, although numerous exceptions exist where the methylation status of both L1 and Alu insertions leak into nearby regions, leading to either methylation spreading or hypomethylation sloping shores. In conclusion, we demonstrated the methylation calling capability of third-generation sequencing and its unique advantage in characterizing epigenomic features within non-reference positions. While TE insertions primarily exhibit methylation patterns restricted within their boundaries, some TEs are able to engage in context-dependent complex interactions with genomic neighborhood.\n\nCharacterizing cytosine methylation of polymorphic human transposable element insertions using human pangenome resources", "token_count": 468, "char_count": 2150, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:35.836511", "source": {"split": "train_shard_00001", "doc_id": 654}, "chunk_id": "train_shard_00001_654_0", "global_id": 6579}
{"text": "<i>Fusarium circinatum</i> is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of <i>F. circinatum</i>. These genomes were analysed together with previously published genomes of <i>F. circinatum</i> isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.\n\nIntra-Species Genomic Variation in the Pine Pathogen <i>Fusarium circinatum</i>.", "token_count": 379, "char_count": 1494, "word_count": 215, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": {"genes": ["FSP34", "KS17"], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:36.392686", "source": {"split": "train_shard_00001", "doc_id": 655}, "chunk_id": "train_shard_00001_655_0", "global_id": 6580}
{"text": "<h4>Background and objectives</h4>Probiotics are defined as live micro-organisms conferring a health benefit on the host. Although most probiotics are bacteria, some yeasts such as <i>Saccharomyces</i> and <i>Kluyveromyces</i>, has been found to have effective probiotic properties. The objective of this study was to isolate and identify indigenous <i>Saccharomyces</i> and <i>Kluyveromyces</i> yeast strains and to compare some probiotic characteristics between these two strains <i>in vitro</i>.<h4>Materials and methods</h4>Strains were isolated on yeast glucose chloramphenicol agar medium from 205 samples and identified by morphological, physiological and biochemical assays. The effects of different conditions such as pH and temperature on the survival and growth of the isolates were studied. In addition, resistance to acidic pH (1.5, 2, 3 and 5), pepsin and different concentrations of bile salts (1%, 3% and 5%), as well as proteolytic, lipolytic and hemolytic activity of selected isolates were assessed. Finally, the best isolates were selected for investigation of their viability in samples of dairy products.<h4>Results</h4>126 isolates were identified using biochemical and molecular techniques as yeast strains. Five isolates were found to have effective probiotic properties, belonging to <i>Kluyveromyces marxianus</i> (S97, S101 and S106) and <i>Saccharomyces cerevisiae</i> (S28, S34). These isolates were able to grow at 37°C, pH=1.5, withstand to concentration of 5% oxbile and pepsin and exhibit the proteolytic activity. The isolates of <i>K. marxianus</i> showed better viability in dairy (yogurt).<h4>Conclusion</h4>In the <i>in-vitro</i> comparative experiments, the isolates of <i>K", "token_count": 520, "char_count": 1714, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "yeast", "saccharomyces"], "conditions": ["acid", "bile", "ph", "temperature"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:37.037925", "source": {"split": "train_shard_00001", "doc_id": 656}, "chunk_id": "train_shard_00001_656_0", "global_id": 6581}
{"text": "marxianus</i> showed better probiotic potentials.\n\nScreening and characterization of <i>in-vitro</i> probiotic criteria of <i>Saccharomyces</i> and <i>Kluyveromyces</i> strains.", "token_count": 67, "char_count": 177, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": ["marxianus", "kluyveromyces", "saccharomyces"], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:37.400198", "source": {"split": "train_shard_00001", "doc_id": 656}, "chunk_id": "train_shard_00001_656_1", "global_id": 6582}
{"text": "Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal in the diversity of terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome of the <i>Gossypium</i> genus by integrating the genomes of 17 diploid and 10 tetraploid species. Within this pangenome, 208 <i>TPS</i> syntelog groups (SGs) were identified, comprising 2 core SGs (TPS5 and TPS42) present in all 27 analyzed genomes, 6 softcore SGs (TPS11, TPS12, TPS13, TPS35, TPS37, and TPS47) found in 25 to 26 genomes, 131 dispensable SGs identified in 2 to 24 genomes, and 69 private SGs exclusive to a single genome. The mutational load analysis of these identified <i>TPS</i> genes across 216 cotton accessions revealed a great number of splicing variants and complex splicing patterns. The nonsynonymous/synonymous Ka/Ks value for all 52 analyzed <i>TPS</i> SGs was less than one, indicating that these genes were subject to purifying selection. Of 208 <i>TPS</i> SGs encompassing 1795 genes, 362 genes derived from 102 SGs were identified as atypical and truncated. The structural analysis of <i>TPS</i> genes revealed that gene truncation is a major mechanism contributing to the formation of atypical genes. An integrated analysis of three RNA-seq datasets from cotton plants subjected to herbivore infestation highlighted nine upregulated <i>TPSs</i>, which included six previously characterized <i>TPSs</i> in <i>G", "token_count": 471, "char_count": 1464, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6698, "quality_score": 0.8349, "entities": {"genes": ["TPS47", "TPS11", "TPS42", "TPS13", "TPS5", "TPS37", "TPS35", "TPS12"], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:38.056621", "source": {"split": "train_shard_00001", "doc_id": 657}, "chunk_id": "train_shard_00001_657_0", "global_id": 6583}
{"text": "hirsutum</i> (<i>AD1_TPS10</i>, <i>AD1_TPS12</i>, <i>AD1_TPS40</i>, <i>AD1_TPS42</i>, <i>AD1_TPS89</i>, and <i>AD1_TPS104</i>), two private <i>TPSs</i> (<i>AD1_TPS100</i> and <i>AD2_TPS125</i>), and one atypical <i>TPS</i> (<i>AD2_TPS41</i>). Also, a TPS-associated coexpression module of eight genes involved in the terpenoid biosynthesis pathway was identified in the transcriptomic data of herbivore-infested <i>G. hirsutum</i>. These findings will help us understand the contributions of <i>TPS</i> family members to interspecific terpene chemotypes within <i>Gossypium</i> and offer valuable resources for breeding insect-resistant cotton cultivars.\n\nPangenome Identification and Analysis of Terpene Synthase Gene Family Members in <i>Gossypium</i>.", "token_count": 298, "char_count": 754, "word_count": 82, "semantic_coherence": 1, "information_density": 0.8171, "quality_score": 0.9085, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:38.594155", "source": {"split": "train_shard_00001", "doc_id": 657}, "chunk_id": "train_shard_00001_657_1", "global_id": 6584}
{"text": "<h4>Motivation</h4>As genomics data analysis becomes increasingly intricate, researchers face the challenge of mastering various software tools. The rise of Pangenomics analysis, which examines the complete set of genes in a group of genomes, is particularly transformative in understanding genetic diversity. Our interdisciplinary team of biologists and mathematicians developed a short Pangenomics Workshop covering Bash, Python scripting, Pangenome, and Topological Data Analysis. These skills provide deeper insights into genetic variations and their implications in Evolutionary Biology. The workshop uses a Conda environment for reproducibility and accessibility. Developed in The Carpentries Incubator infrastructure, the workshop aims to equip researchers with essential skills for Pangenomics research. By emphasizing the role of a community of practice, this work underscores its significance in empowering multidisciplinary professionals to collaboratively develop training that adheres to best practices.<h4>Results</h4>Our workshop delivers tangible outcomes by enhancing the skill sets of Computational Biology professionals. Participants gain hands-on experience using real data from the first described pangenome. We share our paths toward creating an open-source, multidisciplinary, and public resource where learners can develop expertise in Pangenomic Analysis. This initiative goes beyond advancing individual capabilities, aligning with the broader mission of addressing educational needs in Computational Biology.<h4>Availability and implementation</h4>https://carpentries-incubator.github.io/pangenomics-workshop/.\n\nMeeting the challenge of genomic analysis: a collaboratively developed workshop for pangenomics and topological data analysis.", "token_count": 372, "char_count": 1765, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6934, "quality_score": 0.8467, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:39.155549", "source": {"split": "train_shard_00001", "doc_id": 658}, "chunk_id": "train_shard_00001_658_0", "global_id": 6585}
{"text": "<title>Abstract</title>  <p><italic>Staphylococcus aureus</italic> ST398 is a typical ‘One Health’ pathobiont exemplifying multiple-host tropisms. Here we traced the evolutionary trajectory of the global accessory genome (an assembly of accessory genes) of <italic>S. aureus</italic> ST398 over 20 years, with the aim of identifying the mechanisms linking accessory genomes with multiple-host tropisms and the phylogenomic traits associated with severe human infections. We analyzed 1079 high-quality genomes of ST398 from 13 host species, spanning 23 years (1998–2021) and 25 countries across 5 continents, and showed that accessory gene pools of ST398 substantially expanded in the early period before 2010, aligning with the increase in the host-species spectrum. The more recent shifts of accessory genomes were mainly driven by stochastic processes. Accessory genes transferred widely across ST398 from different host-species and barely formed host-specific accessory gene pools, indicating that a host-jump of ST398 was followed shortly by another host-switch rather than a long-term co-evolution with a new host species to generate host-specific gene pools. Human-ST398 was a major recipient of accessory gene transfer, with more common gene transfer with ST398 from pig than other animals. Life-threatening exotoxin genes separately encoding Panton-Valentine Leukocidin and the staphylococcal enterotoxin B were abundant and exclusive to human-ST398 that showed a higher evolution rate than animal-ST398. Both accessory and core genome analyses implied nutrient metabolism as a major force for ST398 evolution. Analyses of clinical data revealed a conserved evolution of ST398 along infection development within a patient, and identified a novel subtype ST398-9 (a relatively recent phylogenetic branch) and phages StauST398_5 and StauST398_1 to be closely associated with human infections", "token_count": 508, "char_count": 1897, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": {"genes": ["ST398"], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:39.791087", "source": {"split": "train_shard_00001", "doc_id": 659}, "chunk_id": "train_shard_00001_659_0", "global_id": 6586}
{"text": "Our findings elucidate mechanisms underlying the distribution and evolution of accessory gene pools of ST398, which determine the development of multiple-host tropisms and pathogenicity.</p>\n\nFrequent host-switch and gene exchange shape the evolution of Staphylococcus aureus ST398", "token_count": 69, "char_count": 281, "word_count": 36, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": {"genes": ["ST398"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:40.146481", "source": {"split": "train_shard_00001", "doc_id": 659}, "chunk_id": "train_shard_00001_659_1", "global_id": 6587}
{"text": "One approach to sustainable agricultural production in a changing global environment is the effective utilization of unutilized germplasms. Among these, crop wild relatives (CWRs) represent valuable germplasms that retain the diversity lost during domestication. The genus <i>Oryza</i> has two cultivated species and 22 wild species. One of the cultivated species, <i>Oryza sativa</i>, produces the rice that is the staple food for half of the world's population. We are responsible for the maintenance and distribution of wild <i>Oryza</i> genetic resources held by Japan's National Institute of Genetics (NIG). The NIG has collected the genome sequences of numerous wild <i>Oryza</i> accessions, aiming at understanding and promoting the utilization of <i>Oryza</i> germplasm for both basic and applied sciences, such as breeding. The genome information of many wild <i>Oryza</i> germplasms deciphered by multiple groups is publicly available in databases, allowing for pangenome analysis. This review mainly introduces the wild <i>Oryza</i> genetic resources held by the NIG, discusses the genome diversity revealed through genome sequencing, presents new attempts to utilize wild <i>Oryza</i> germplasm as novel resources enabled by genome sequencing, and discusses the challenges in further effectively utilizing wild <i>Oryza</i> germplasm in breeding.\n\nUsage of wild &lt;i&gt;Oryza&lt;/i&gt; germplasms for breeding in pan-genomics era.", "token_count": 373, "char_count": 1443, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:40.706890", "source": {"split": "train_shard_00001", "doc_id": 660}, "chunk_id": "train_shard_00001_660_0", "global_id": 6588}
{"text": "Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate significantly in gene content. However, due to the transient and hypervariable nature of many accessory elements, the value of the added resolution in outbreak investigations remains disputed. To assess the analytical value of bacterial accessory genomes in clustering epidemiologically related cases, we trained classifiers on a set of genomes collected from 24 <i>Salmonella enterica</i> outbreaks of food, animal, or environmental origin. The models demonstrated high precision and recall on unseen test data with near-perfect accuracy in classifying clonal and short-term outbreaks. Annotating the genomic features important for cluster classification revealed functional enrichment of molecular fingerprints in genes involved in membrane transportation, trafficking, and carbohydrate metabolism. Importantly, we discovered polymorphisms in mobile genetic elements (MGEs) and gain/loss of MGEs to be informative in defining outbreak clusters. To quantify the ability of MGE variations to cluster outbreak clones, we devised a reference-free tree-building algorithm inspired by colored de Bruijn graphs, which enabled topological comparisons between MGE and standard typing methods. Systematic evaluation of clustering MGEs on an unseen dataset of 34 <i>Salmonella</i> outbreaks yielded mixed results that exemplified the power of accessory sequence variations when core genomes of unrelated cases are insufficiently discriminatory, as well as the distortion of outbreak signals by microevolution events or the incomplete assembly of MGEs.<h4>Importance</h4>Gene-by-gene typing is widely used to detect clusters of foodborne illnesses that share a common origin. It remains actively debated whether the inclusion of accessory sequences in bacterial typing schema is informative or deleterious for cluster definitions in outbreak investigations due to the potential confounding effects of horizontal gene transfer. By training machine learning models on a curated set of historical <i>Salmonella</i> outbreaks, we revealed an enriched presence of outbreak distinguishing features in a wide range of mobile genetic elements", "token_count": 521, "char_count": 2416, "word_count": 327, "semantic_coherence": 1, "information_density": 0.6147, "quality_score": 0.8073, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["bile", "ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:41.334949", "source": {"split": "train_shard_00001", "doc_id": 661}, "chunk_id": "train_shard_00001_661_0", "global_id": 6589}
{"text": "Systematic comparison of the efficacy of clustering different accessory elements against standard sequence typing methods led to our cataloging of scenarios where accessory sequence variations were beneficial and uninformative to resolving outbreak clusters. The presented work underscores the complexity of the molecular trends in enteric outbreaks and seeks to inspire novel computational ways to exploit whole-genome sequencing data in enteric disease surveillance and management.\n\nMachine learning reveals the dynamic importance of accessory sequences for &lt;i&gt;Salmonella&lt;/i&gt; outbreak clustering.", "token_count": 124, "char_count": 610, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7532, "quality_score": 0.8766, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:41.703214", "source": {"split": "train_shard_00001", "doc_id": 661}, "chunk_id": "train_shard_00001_661_1", "global_id": 6590}
{"text": "A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection", "token_count": 21, "char_count": 132, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:42.056708", "source": {"split": "train_shard_00001", "doc_id": 662}, "chunk_id": "train_shard_00001_662_0", "global_id": 6591}
{"text": "<h4>Introduction</h4><i>Cutibacterium acnes</i> can both be a helpful colonizer of the human skin as well as the causative agent of acne and purulent infections. Until today, it is a moot point whether there are <i>C. acnes</i> strains exclusively devoted to be part of the skin microbiome and others, that carry special features enabling them to cause disease. So far, the search for the molecular background of such diverse behavior has led to inconsistent results.<h4>Methods</h4>In the present study, we prospectively collected <i>C. acnes</i> strains from 27 infected persons and 18 healthy controls employing rigid selection criteria to ensure their role as infectious agent or colonizer. The genome sequences from these strains were obtained and carefully controlled for quality.<h4>Results</h4>Deduced traditional phylotyping assigned almost all superficial isolates to type IA1, while the clinical strains were evenly distributed between types IA1, IB, and II. Single locus sequence typing (SLST) showed a predominance of A1 type for the control strains, whereas 56% of the clinical isolates belonged to types A1, H1 and K8. Pangenome analysis from all the present strains and 30 published genomes indicated the presence of an open pangenome. Except for three isolates, the colonizing strains clustered in clades separate from the majority of clinical strains, while 4 clinical strains clustered with the control strains. Identical results were obtained by a single nucleotide polymorphism (SNP) analysis. However, there were no significant differences in virulence gene contents in both groups.<h4>Discussion</h4>Genome-wide association studies (GWAS) from both the pangenome and SNP data consistently showed genomic differences between both groups located in metabolic pathway and DNA repair genes. Thus, the different behavior of colonizing and infectious C. acnes strains could be due to special metabolic capacities or flexibilities rather than specific virulence traits.\n\nWhole genome sequencing distinguishes skin colonizing from infection-associated <i>Cutibacterium acnes</i> isolates.", "token_count": 513, "char_count": 2103, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": {"genes": ["IA1"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": false, "timestamp": "2025-10-31T21:44:42.659391", "source": {"split": "train_shard_00001", "doc_id": 663}, "chunk_id": "train_shard_00001_663_0", "global_id": 6592}
{"text": "Invasive gastric candidiasis is a rare fungal infection of the stomach, often arising in the setting of immunosuppression, critical illness, mucosal barrier disruption, gut microbial alterations, or antibiotic use. Though <i>Candida spp.</i> are normal flora within the gastrointestinal tract, compromised host defenses can contribute to overgrowth and invasion of the fungal species into deeper tissues. We report a case of an 89-year-old man presenting with concurrent upper gastrointestinal bleeding from diffuse gastric ulcers secondary to invasive gastric candidiasis and diarrhea resulting from <i>Clostridioides difficile</i> colitis. The pathophysiology, diagnosis, and management of invasive candidiasis as well as interactions between gastrointestinal candidiasis and <i>Clostridioides difficile</i> infection are discussed. Overall, this case highlights the interplay between antibiotic use, gut barrier translocation, interactions between microorganisms, and worsening infectious disease in an elderly patient. Similarly, it stresses the importance of maintaining a high index of suspicion for fungal infections in patients with large atypical appearing gastric ulcers, even in the absence of overt immunosuppression.\n\nInvasive Gastric Candidiasis With Concurrent Clostridioides difficile Colitis: A Case Report and Review of the Literature.", "token_count": 341, "char_count": 1353, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["gut", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:43.217314", "source": {"split": "train_shard_00001", "doc_id": 664}, "chunk_id": "train_shard_00001_664_0", "global_id": 6593}
{"text": "<h4>Background</h4>Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges.<h4>Results</h4>Our study evaluates recommended data types and volumes required to establish a robust de novo genome assembly pipeline for population-level pangenome projects, extensively examining performance between ONT's Duplex and PacBio HiFi datasets in the context of achieving high-quality phased genomes with enhanced contiguity and completeness. The results show that achieving chromosome-level haplotype-resolved assembly requires 20 × high-quality long reads such as PacBio HiFi or ONT Duplex, combined with 15-20 × of ultra-long ONT per haplotype and 10 × of long-range data such as Omni-C or Hi-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in phasing accuracies, while Duplex generates more T2T contigs.<h4>Conclusion</h4>Our study provides insights into optimal data types and volumes for robust de novo genome assembly in population-level pangenome projects. Reassessing the recommended data types and volumes in this study and aligning them with practical economic limitations are vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.\n\nEvaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.", "token_count": 482, "char_count": 2010, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:43.834233", "source": {"split": "train_shard_00001", "doc_id": 665}, "chunk_id": "train_shard_00001_665_0", "global_id": 6594}
{"text": "Prophages play a crucial role in shaping host physiology, influencing traits such as virulence and antimicrobial resistance. In Salmonella enterica , prophages can constitute up to 30% of the accessory genome, contributing significantly to its genetic diversity and adaptability. In this study, we employed an in-silico approach to identify prophages within S. enterica genomes obtained poultry and clinical isolates. A total of 151 S. enterica sequences were assembled using SPAdes and subsequently quality-filtered with Abyss and BUSCO. Prophage sequences were detected using Phigaro and CheckV, followed by quality assessment with PHASTEST. The identification was performed using a custom database comprising 60 S. enterica prophages from previous studies. Comparative genomics, including gene annotation and recombination detection, were performed on representative prophages. Virulence genes were identified using VFDB and VirulenceFinder databases. Lastly, phylogenetic analysis of the prophages was carried out based on terminase and integrase sequences. We obtained 142 S. enterica genomes to analyze their prophage content. Peduovirus pro483 was highly prevalent among S. Infantis isolates and carried two cargo proteins: an Imma/Irre metalloendopeptidase and a fimbrial protein. In contrast, a related S. Enteritidis isolate also harboring Peduovirus pro483 carried a different set of cargo genes—HEPN-MAE-28990 and a cytosine-specific methyltransferase—suggesting horizontal transfer or a recent phage acquisition event. Enterobacteria phage ST104 , found in S. Typhimurium, exhibited nearly complete identity to its reference and encoded superinfection exclusion proteins (SieA, SieB), enhancing phage resistance. Phylogenetic analyses supported their classification and revealed distinct evolutionary relationships tied to host serovar and environment. To our knowledge, this is the first study to describe prophage diversity in S. enterica strains isolated from Ecuadorian poultry farms, providing insights into their potential role in strain adaptation and public health relevance.", "token_count": 509, "char_count": 2096, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.831, "entities": {"genes": ["ST104"], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:44.461968", "source": {"split": "train_shard_00001", "doc_id": 666}, "chunk_id": "train_shard_00001_666_0", "global_id": 6595}
{"text": "Exploring prophages in <i>Salmonella enterica</i>: an <i>in-silico</i> approach", "token_count": 29, "char_count": 79, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:44.808035", "source": {"split": "train_shard_00001", "doc_id": 666}, "chunk_id": "train_shard_00001_666_1", "global_id": 6596}
{"text": "Bacterial exopolysaccharides (EPS) have emerged as one of the key players in the field of heavy metal-contaminated environmental bioremediation. This study aimed to characterize and evaluate the metal biosorption potential of EPS produced by a novel <i>Psychrobacillus</i> strain, NEAU-3TGS, isolated from an iron ore deposit at Tamra iron mine, northern Tunisia. Genomic and pan-genomic analysis of NEAU-3TGS bacterium with nine validated published <i>Psychrobacillus</i> species was also performed. The results showed that the NEAU-3TGS genome (4.48 Mb) had a mean GC content of 36%, 4,243 coding sequences and 14 RNA genes. Phylogenomic analysis and calculation of nucleotide identity (ANI) values (less than 95% for new species with all strains) confirmed that NEAU-3TGS represents a potential new species. Pangenomic analysis revealed that <i>Psychrobacillus</i> genomic diversity represents an \"open\" pangenome model with 33,091 homologous genes, including 65 core, 3,738 shell, and 29,288 cloud genes. Structural EPS characterization by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy showed uronic acid and α-1,4-glycosidic bonds as dominant components of the EPS. X-ray diffraction (XRD) analysis revealed the presence of chitin, chitosan, and calcite CaCO<sub>3</sub> and confirmed the amorphous nature of the EPS. Heavy metal bioabsorption assessment showed that iron and lead were more adsorbed than copper and cadmium. Notably, the optimum activity was observed at 37°C, pH=7 and after 3 h contact of EPS with each metal. Genomic insights on iron acquisition and metabolism in <i>Psychrobacillus</i> sp", "token_count": 487, "char_count": 1647, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6913, "quality_score": 0.8457, "entities": {"genes": [], "proteins": [], "pathways": ["metabolism"], "organisms": [], "conditions": ["acid", "ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:45.426303", "source": {"split": "train_shard_00001", "doc_id": 667}, "chunk_id": "train_shard_00001_667_0", "global_id": 6597}
{"text": "NEAU-3TGS suggested that no genes involved in siderophore biosynthesis were found, and only the gene cluster <i>Feu</i>ABCD and trilactone hydrolase genes involved in the uptake of siderophores, iron transporter and exporter are present. Molecular modelling and docking of <i>Feu</i>A (protein peptidoglycan siderophore-binding protein) and siderophores ferrienterobactine [Fe<sup>+3</sup> (ENT)]<sup>-3</sup> and ferribacillibactine [Fe<sup>+3</sup> (BB)]<sup>-3</sup> ligand revealed that [Fe<sup>+3</sup> (ENT)]<sup>-3</sup> binds to Phe122, Lys127, Ile100, Gln314, Arg215, Arg217, and Gln252. Almost the same for [Fe<sup>+3</sup> (ENT)]<sup>-3</sup> in addition to Cys222 and Tyr229, but not Ile100.To the best of our knowledge, this is the first report on the characterization of EPS and the adsorption of heavy metals by <i>Psychrobacillus</i> species. The heavy metal removal capabilities may be advantageous for using these organisms in metal remediation.\n\nGenome and pan-genome analysis of a new exopolysaccharide-producing bacterium <i>Pyschrobacillus</i> sp. isolated from iron ores deposit and insights into iron uptake.", "token_count": 401, "char_count": 1132, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7254, "quality_score": 0.8627, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": ["ph"]}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:46.016784", "source": {"split": "train_shard_00001", "doc_id": 667}, "chunk_id": "train_shard_00001_667_1", "global_id": 6598}
{"text": "Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) [ https://github.com/IndraGonz/CLARC ] improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8,000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by more than 30% and improved evolutionary predictions based on accessory gene frequencies. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.\n\nLinkage-based ortholog refinement in bacterial pangenomes with CLARC", "token_count": 242, "char_count": 1039, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7519, "quality_score": 0.876, "entities": {"genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": []}, "biobert_ready": true, "timestamp": "2025-10-31T21:44:46.480554", "source": {"split": "train_shard_00001", "doc_id": 668}, "chunk_id": "train_shard_00001_668_0", "global_id": 6599}