The Ability of Taxonomic Identification of Bifidobacteria Based on the Variable Regions of 16S rRNA Gene
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TICS OF MICROORGANISMS
The Ability of Taxonomic Identification of Bifidobacteria Based on the Variable Regions of 16S rRNA Gene E. S. Klimenkoa, *, A. V. Pogodinaa, L. V. Rychkovaa, and N. L. Belkovaa aScientific
Center for Family Health and Human Reproduction Problems, Irkutsk, 664003 Russia *e-mail: [email protected]
Received September 11, 2019; revised January 16, 2020; accepted January 23, 2020
Abstract—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. Keywords: bifidobacteria, intestinal microbiome, 16S rRNA gene, variable regions, ribosomal taxonomy, high throughput sequencing DOI: 10.1134/S1022795420080074
INTRODUCTION Bifidobacteria are considered key commensals of the human intestine, which play an important role in maintaining a person’s health [1]. More than 60 species and subspecies of the genus Bifidobacterium were isolated mainly from five different habitats: the intestines of humans, insects, and animals, the human oral cavity, and wastewater. The presence of bifidobacteria DNA in human blood was also noted [2, 3]. The diversity of habitats reflects the ecological origin of bifidobacteria, which is primarily associated with intestinal microbiota. Bifidobacteria dominate the human intestines in the very early stages of life and are the first to respond to any stress factors, such as antibiotics and toxins. With age, not only a gradual decrease in the representation of bifidobacteria in the total microbiome is noted, but also a change in the population structure [4, 5]. The restructuring of the microbiocenosis of the large intestine is observed during the formation of functional gastrointestinal disorders in children and adolescents [6–8] and as a factor of technogenic pressure [9, 10]. So, for the juvenile population of the city of Irkutsk, four species of bifidobacteria were identified as dominant in the intestinal biotope—Bifidobacterium bifidum, B. catenulatum, B. longum, and B. adolescentis. At the same time, it was found that, in healthy children, multicomponent species associations prevail; in children with functional
gastrointestinal disorders, bifidobacteria grow in a monospecies form [11]. In the 2000s, the introduction of next generation s
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