The Ability of Taxonomic Identification of Bifidobacteria Based on the Variable Regions of 16S rRNA Gene

Bifidobacteria are considered key commensals of the human intestinal tract; they dominate the community in the earliest stages of life and are the first to respond to stress factors. The metasequencing of the V3–V4 16S rRNA fragments made it possible to identify 12 phylotypes of bifidobacteria in the gut microbiome of adolescents, which accounted for from 0.0001 to 0.9% of the total microbiome. A phylogenetic analysis of the obtained phylotypes was conducted; such species as B. angulatum, B. bifidum, B. longum, and B. animalis, as well as subspecies B. animalis subsp. lactis, were identified. The species of bifidobacteria excluded from identification by the V3–V4 variable regions were identified. The phylogenetic analysis of different variable regions and their combinations showed that a tree topology based on the V2 fragment is the most similar to a tree topology based on the complete gene.