Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species

Abstract

Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups – divisions I and II – characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined. Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required. Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies. Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database. Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels. Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis , is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.

Pangenome comparison ofBacteroides fragilisgenomospecies unveil genetic diversity and ecological insights

“…Based on the phylogeny of the core genome alignment by maximum likelihood, midpoint-rooted, divisions I and II also separate into discrete clades (Figure 1F) . Collectively, these analyses reinforce the recent proposal to classify B. fragilis division II strains as a novel species (Wallace et al, 2022; English et al, 2023).…”

“…Bacteroides fragilis is a persistent colonizer of the human gut and has been linked to both health and disease (Wexler, 2007). Multiple studies have reported two distinct, monophyletic groups within B. fragilis , referred to as division I and division II, which share 87% average nucleotide identity, while the typical species cutoff is 96% (Johnson, 1978; Podglajen et al, 1995; Ruimy et al, 1996; Gutacker et al, 2000; Nagy et al, 2011; Wallace et al, 2022; English et al, 2023). Here, we use comparative genomics to identify the genetic differences between division I and II strains, to provide further evidence for the classification of these divisions as two distinct species (Wallace et al, 2022; English et al, 2023).…”

“…Multiple studies have reported two distinct, monophyletic groups within B. fragilis , referred to as division I and division II, which share 87% average nucleotide identity, while the typical species cutoff is 96% (Johnson, 1978; Podglajen et al, 1995; Ruimy et al, 1996; Gutacker et al, 2000; Nagy et al, 2011; Wallace et al, 2022; English et al, 2023). Here, we use comparative genomics to identify the genetic differences between division I and II strains, to provide further evidence for the classification of these divisions as two distinct species (Wallace et al, 2022; English et al, 2023). We examined genes conserved within each division, but not between divisions, which likely play a fundamental role in their biology and function within their respective niches.…”

Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights

“…They have primarily been differentiated through the presence of cepA , a beta-lactamase, which is unique to division I ( 2 ), and the chromosomally encoded carbapenemase gene ( cfiA or ccrA ), which is unique to division II and provides resistance to beta-lactamase inhibitors ( 3 , 4 ). Due to their genetic similarity, traditional methods such as 16S rRNA gene analysis cannot distinguish between these divisions, yet they share an average nucleotide identity (ANI) of 87%, below the typical species cutoff of 96% ( 3 , 5 – 10 ). Here, we conduct a comprehensive genomic comparison and identified genes conserved within each B. fragilis division, but not shared between them, shedding light on the unique biological roles and functions of these divisions within their ecological niches.…”