Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota

Bifidobacterium longum subsp. longum is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional divers...

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Bibliographic Details
Published in:Microorganisms (Basel) 2021-09, Vol.9 (9), p.1906
Main Authors: Díaz, Romina, Torres-Miranda, Alexis, Orellana, Guillermo, Garrido, Daniel
Format: Article
Language:English
Subjects:
Adaptation
Annotations
Bifidobacterium longum
Bifidobacterium longum subsp. longum
Breast milk
Carbohydrates
Carbon sources
Cluster analysis
comparative genomics
Digestive system
Divergence
Enzymes
Gastrointestinal tract
Genes
Genomes
Genomic analysis
Genomics
Glycosidases
Glycosyl hydrolase
human gut microbiota
Intestinal microflora
Intestine
Microbiomes
Microbiota
Microorganisms
Niches
Oligosaccharides
Phenols
Phylogenetics
Phylogeny
Young adults
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Summary:Bifidobacterium longum subsp. longum is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies longum, as observed in phylogenetic analysis. B. longum SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among longum subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that B. longum M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of B. longum subsp. longum to colonize the human gut microbiota.
ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms9091906