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.

中文翻译：

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脆弱拟杆菌的基因组分析：I 类和 II 类代表不同的物种

介绍。 脆弱拟杆菌是一种革兰氏阴性厌氧菌，是人类胃肠道微生物群的一员，经常作为肠外机会性病原体被发现。脆弱拟杆菌由两个不同的群体组成——I区和II区——其特征是存在/不存在基因[分别是cepA和ccrA ( cfiA )]，这些基因通过丝氨酸或金属-β-内酰胺酶的产生而赋予对β-内酰胺抗生素的抗性。尚未对公开的脆弱拟杆菌序列数据进行大规模分析，并且该物种的抗性组仍不清楚。假设/差距陈述。已提议将I 类和 II 类B. fragilis重新分类为两个不同的物种，但需要更多证据。目标。研究 GenBank脆弱拟杆菌基因组的基因组多样性，并确定公开可用的脆弱拟杆菌基因组中 I 型和 II 型菌株的流行率，并生成进一步的证据来证明I 型和 II 型脆弱拟杆菌菌株代表不同的基因种。方法。GenBank 中列为脆弱拟杆菌的高质量 ( n = 377) 基因组被纳入泛基因组和功能分析中。基因组数据还使用综合抗生素耐药性数据库进行耐药组分析。结果。平均核苷酸同一性和系统发育分析显示，B. fragilis I 和 II 类代表不同的物种：分别是B. fragilis sensu stricto（n = 275 个基因组）和B. fragilis A（n = 102 个基因组；基因组分类数据库名称）。对 B. fragilis sensu stricto和B. fragilis A全基因组的探索揭示了这两个物种在核心和辅助基因水平上的分离。结论。研究结果表明，B. fragilis A（以前称为 II 类B. fragilis）是一个独立物种，与B. fragilis sensu stricto不同。脆弱拟杆菌全基因组分析支持了之前的基因组、系统发育和抗性组筛选分析，共同强化了 I 类和 II 类是两个独立的物种。此外，还证实了脆弱拟杆菌辅助基因的差异 I 和 II 类主要与碳水化合物代谢相关，表明除抗菌素耐药性之外的差异也可用于区分这两个物种。