{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T01:12:18Z","timestamp":1784077938588,"version":"3.55.0"},"reference-count":121,"publisher":"Microbiology Society","issue":"11","license":[{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"\n Introduction.<\/jats:bold>\n \n \n Bacteroides fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> comprises two distinct groups \u2013 divisions I and II \u2013 characterized by the presence\/absence of genes [cepA<\/jats:italic> and ccrA<\/jats:italic> (cfiA<\/jats:italic>), respectively] that confer resistance to \u03b2-lactam antibiotics by either serine or metallo-\u03b2-lactamase production. No large-scale analyses of publicly available \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> sequence data have been undertaken, and the resistome of the species remains poorly defined.<\/jats:p>\n \n Hypothesis\/Gap Statement.<\/jats:bold> Reclassification of divisions I and II \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> as two distinct species has been proposed but additional evidence is required.<\/jats:p>\n \n Aims<\/jats:bold>. To investigate the genomic diversity of GenBank \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> genomes and establish the prevalence of division I and II strains among publicly available \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> genomes, and to generate further evidence to demonstrate that \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> division I and II strains represent distinct genomospecies.<\/jats:p>\n \n Methodology<\/jats:bold>. High-quality (n<\/jats:italic>=377) genomes listed as \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.<\/jats:p>\n \n Results.<\/jats:bold> Average nucleotide identity and phylogenetic analyses showed \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> divisions I and II represent distinct species: B. fragilis sensu stricto<\/jats:italic> (n<\/jats:italic>=275 genomes) and \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> A (n<\/jats:italic>=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto<\/jats:italic> and \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> A revealed separation of the two species at the core and accessory gene levels.<\/jats:p>\n \n Conclusion<\/jats:bold>. The findings indicate that \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> A, previously referred to as division II \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic>, is an individual species and distinct from B. fragilis sensu stricto<\/jats:italic>. The \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> 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 \n \n B. fragilis<\/jats:ext-link>\n <\/jats:named-content>\n <\/jats:italic> 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.<\/jats:p>","DOI":"10.1099\/jmm.0.001768","type":"journal-article","created":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T16:01:18Z","timestamp":1698854478000},"source":"Crossref","is-referenced-by-count":18,"title":["Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species"],"prefix":"10.1099","volume":"72","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7491-1366","authenticated-orcid":false,"given":"Jamie","family":"English","sequence":"first","affiliation":[{"name":"Institute for Global Food Security, School of Biological Sciences, Queen\u2019s University, Belfast, 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