Comprehensive Phylogenomic Analyses Support the Reclassification of Multiple Bacteroides Species

Bacteroides are among the most dominant members of the human gut microbiota, contributing significantly to host metabolism, immune regulation, and intestinal homeostasis. Despite their beneficial roles, several Bacteroides are also known as opportunistic pathogens. Despite their clinical and ecological significance, taxonomic resolution within this genus remains challenging due to the high genetic similarity among closely related species. In this study, we conducted a comprehensive comparative analysis of the genomic, phylogenetic, and phenotypic characteristics of multiple Bacteroides to clarify their taxonomic relationships including B. humanifaecis, B. rhinocerotis, B. parvus, B. koreensis, B. kribbi, and B. ovatus. Phylogenetic analysis based on 16 S rRNA gene sequences revealed high sequence similarity among the species. Genomic comparisons using overall genome relatedness indices (OGRIs), including average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH), consistently exceeded species delineation thresholds, with ANI values ranging from 98.4% to 99.6%, dDDH values exceeded the 70%, and AAI values ranged from 98.1% to 99.5%. These findings were further supported by shared phenotypic and metabolic traits, including similar enzymatic activities and carbohydrate utilization profiles. Based on this evidence, we propose the reclassification of Bacteroides humanifaecis Kim et al. 2023 and Bacteroides rhinocerotis Li et al. 2024 as later heterotypic synonyms of Bacteroides parvus Liu et al. 2022, and Bacteroides koreensis Shin et al. 2017 and Bacteroides kribbi Shin et al. 2017 as later heterotypic synonyms of Bacteroides ovatus Eggerth and Gagnon 1933 (Approved Lists 1980).