Comparative Evolutionary Genomics Reveals Genetic Diversity and Differentiation in Bacteroides fragilis
Bibliographic record
Abstract
Background/Objectives: Bacteroides fragilis is the pathogenic anaerobe most commonly isolated from intra-abdominal infections, abscesses, and blood. Despite its clinical importance, research on its pan-genome-scale evolution is still limited. Methods: Herein, we analyzed the pan-genome architecture of 374 B. fragilis strains to explore their intra-species genomic diversity and evolutionary patterns. Results: Our analysis revealed an open pan-genome with a high proportion of accessory genomes, indicating high genetic variability. Accessory genome genes were substantially enriched in the functions of “Replication, Recombination, and Repair” suggesting their roles in gene transfer and divergence. Phylogenomic analysis divided B. fragilis into two distinct clades: divisions I and II, differing in gene content, antimicrobial resistance genes, and mobile genetic elements. Division II revealed higher Tajima’s D values, suggesting that it separated after B. fragilis’s recent species diversification. The extreme shift in the distribution of gene-wise Hudson’s fixation index (Fst) values for each division suggested that several genes are highly differentiated or evolved between the two clades. Average nucleotide identity and 16S rRNA analyses showed that B. fragilis division II represents a distinct species, Bacteroides hominis. Additionally, a considerable depletion of recombination in genes with Fst values > 0.99 was noted, suggesting that the highest Fst genes with little recombination are the basis for differentiation between divisions. Conclusions: Overall, this study enhances the understanding of B. fragilis’s genomic diversity, evolutionary dynamics, and potential role in pathogenesis, shedding light on its adaptation and diversification.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".