Using Whole-Genome Sequencing to Revise the Classification of the Bifidobacterium and Gardnerella Genera

Most commonly known for their probiotic properties, Bifidobacteria are gram-positive, rod-shaped, anaerobic bacteria often found in the digestive tracts of various mammals and insects. Belonging to the same family as Bifidobacterium, Gardnerella comprises a single species (G. vaginalis) implicated in bacterial vaginosis, whose taxonomic status has often been disputed. Various phylogenetic trees of the Bifidobacteriaceae family place G. vaginalis centrally within the Bifidobacterium genus on the basis of 16S rRNA sequences. Additionally, the discrimination between Gardnerella and Bifidobacterium has proven difficult in the laboratory. In this study, we aim to elucidate the taxonomic position of G. vaginalis and revise the classification of the Bifidobacterium genus through whole-genome sequencing (WGS) of 62 type strains of Bifidobacterium and the type strain of G. vaginalis. To infer their taxonomic relationship to each other, we measured their whole-genome distance and placement within the phylogenetic tree. Within the Bifidobacterium genus, comparative WGS analyses showed close relatedness between seemingly distinct species, and conversely, dissimilarity among the subspecies. We propose the reclassification of B. faecale as a later heterotypic synonym of B. adolescentis. Similarly, we propose the unification of B. gallinarum and B. saeculare as B. gallinarum subsp. gallinarum and B. gallinarum subsp. saeculare, and the unification of B. catenulatum and B. kashiwanohense as B. catenulatum subsp. catenulatum and B. catenulatum subsp. kashiwanohense. In the B. longum subspecies group, we propose the reclassification of B. longum subsp. infantis as its own species, B. infantis, and the reclassification of B. longum subsp. suillum as B. longum subsp. suis. Additionally, insufficient relatedness between B. pseudolongum subsp. pseudolongum and B. pseudolongum subsp. globosum, and between B. animalis subsp. animalis and B. animalis subsp. lactis, indicate the subspecies should be reclassified as their own species. We suggest amending the classification of B. pseudolongum subspecies group to B. pseudolongum and B. globosum, and of B. animalis subspecies group to B. animalis and B. lactis. Distance- and gene-based phylogenetic trees of the type strains position G. vaginalis in the midst of the Bifidobacterium genus, further corroborating the close relatedness between the two genera and providing additional justification for reclassifying Gardnerella vaginalis as a species of Bifidobacterium.