1887

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Volume 72, Issue 11

Genomic analyses of : subdivisions I and II represent distinct species Open Access

Abstract

is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. comprises two distinct groups – divisions I and II – characterized by the presence/absence of genes [ and (), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available sequence data have been undertaken, and the resistome of the species remains poorly defined.

Reclassification of divisions I and II as two distinct species has been proposed but additional evidence is required.

. To investigate the genomic diversity of GenBank genomes and establish the prevalence of division I and II strains among publicly available genomes, and to generate further evidence to demonstrate that division I and II strains represent distinct genomospecies.

. High-quality (=377) genomes listed as in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.

Average nucleotide identity and phylogenetic analyses showed divisions I and II represent distinct species: (=275 genomes) and A (=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of and A revealed separation of the two species at the core and accessory gene levels.

. The findings indicate that A, previously referred to as division II , is an individual species and distinct from . The 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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , Bacteroidaceae and taxonomy
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-11-01
2024-04-27
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Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species
J. Med. Microbiol. 72, 001768 (2023); https://doi.org/10.1099/jmm.0.001768
/content/journal/jmm/10.1099/jmm.0.001768
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