Abstract
BackgroundBifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach.ResultsWe analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO).ConclusionsThe results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.
Highlights
Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, indicative of a close symbiotic host-microbe relationship
In order to facilitate a coherent comparative analysis, we carried out a uniform open reading frame (ORF) prediction for all our 20 sequenced genomes in addition to the fully-sequenced B. longum genomes retrieved from public databases
According to our comparative genomic analysis, the results depict a snapshot of their substantial genetic diversity in terms of genes and predicted Glycosyl hydrolases (GHs), as well as their ability to metabolize a large range of sugars
Summary
Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, indicative of a close symbiotic host-microbe relationship. The human gut microbiota harbours a complex and dynamic microbial community, which plays various functional roles to support human physiology and health [1] This so-called “hidden organ” elicits important metabolic, structural and protective activities, and influences behaviour and brain function through the proposed “gut-brain-axis” [2, 3]. More than 13% of the so-called clusters of orthologous gene (COG) families in the Bifidobacterium pan-genome are associated with carbohydrate metabolism [9] This saccharolytic genotype allows bifidobacteria to metabolize a variety of carbohydrates (host- and diet-derived substrates), which are not digested by the host’s digestive enzymes [10], to provide a competitive advantage in the complex gut environment
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