With the spread of next-generation sequencers, it has become possible to understand the human gut microbiota without performing cultures. Sequencers have revealed that human gut microbiota are composed of a greater variety of bacterial species than has previously been imagined. The phylum Bacteroidetes is one of the predominant groups in human gut microbiota. Most of the members of the phylum Bacteroidetes belong to the families Bacteroidaceae, Porphyromonadaceae, Prevotellaceae and Rikenellaceae. Over the last decade, a large number of novel genera or novel species that belong to the above-mentioned families have been proposed. Recently, applying the large-scale analysis methods developed for cultures to the analysis of the human gut microbiota, has resulted in a number of novel species being proposed. However, it is necessary to be careful when using these scientific names, because some of these bacterial names have not been formally accepted. In this review, the current taxonomy of the genus Bacteroides and related taxa are discussed.
“Bifidobacteria” are a group of Gram-positive polymorphic anaerobic bacteria that are commonly found in the gastrointestinal tracts of humans and animals. These bacteria comprise 58 species in 6 genera of the family Bifidobacteriaceae within the phylum Actinobacteria. Among them, the genus Bifidobacterium, which consists of 50 species and 10 subspecies, is a predominant component of the bifidobacteria. Technical progress in the identification and classification of bacterial species is closely associated with developments in the approaches to bacterial taxonomy. DNA-DNA hybridization (DDH) values have been used since the 1960s to determine the relatedness between strains, and they are still the most important criterion for the delineation of bacterial species. Meanwhile, phylogenetic analysis based on 16S rRNA gene sequences has become a mainstream method in the classification and identification of bacteria, and it is now used as an alternative gold standard to DDH tests, which are time consuming and require expert skills. However, in many cases, members of a group of closely related species are impossible to distinguish on the basis of their 16S rRNA gene sequences alone, because the level of identity among the 16S rRNA gene sequences in these species is considerably higher than the recommended value for species differentiation. In recent years, a number of important methods have been developed as alternatives and complements to DDH, such as the multilocus sequence analysis or typing (MLSA or MLST) and the average nucleotide identity (ANI), which is a method based on the whole genome sequences. This paper briefly describes the current status and trends concerning the methods used for the classification of bifidobacteria.