Abstract
Bifidobacteria are common members of the gastro-intestinal microbiota of a broad range of animal hosts. Their successful adaptation to this particular niche is linked to their saccharolytic metabolism, which is supported by a wide range of glycosyl hydrolases. In the current study a large-scale gene-trait matching (GTM) effort was performed to explore glycan degradation capabilities in B. breve. By correlating the presence/absence of genes and associated genomic clusters with growth/no-growth patterns across a dataset of 20 Bifidobacterium breve strains and nearly 80 different potential growth substrates, we not only validated the approach for a number of previously characterized carbohydrate utilization clusters, but we were also able to discover novel genetic clusters linked to the metabolism of salicin and sucrose. Using GTM, genetic associations were also established for antibiotic resistance and exopolysaccharide production, thereby identifying (novel) bifidobacterial antibiotic resistance markers and showing that the GTM approach is applicable to a variety of phenotypes. Overall, the GTM findings clearly expand our knowledge on members of the B. breve species, in particular how their variable genetic features can be linked to specific phenotypes.
Highlights
Bifidobacteria are common members of the gastro-intestinal microbiota of a broad range of animal hosts
Based on a comparative and pan-genome analysis conducted on thirteen representatives of the B. breve species, variable genetic features were identified that are responsible for strain diversification, including genes involved in host or environment interactions, such as biosynthesis of cell surface-exposed structures
In order to provide an updated and comprehensive estimation of the B. breve pan-genome and to determine which fraction of the total gene content assigned to this species is represented by the 20 assessed strains, a pan-genome analysis was performed among 73 B. breve representatives available in public databases inclusive of the 20 strains which were selected for genetrait matching (GTM) analysis within this study (Supplemental Table S2)
Summary
Bifidobacteria are common members of the gastro-intestinal microbiota of a broad range of animal hosts. It has been shown that the microbiota of healthy newborns is highly populated by ‘infant type’ bifidobacteria, such as Bifidobacterium breve, Bifidobacterium longum spp. longum/infantis and Bifidobacterium bifidum[6,7] In this context, members of these species are believed to play a crucial role in the healthy development of the infant gut[8,9,10]. Bifidobacteria rely on diet- and/or host-derived glycans (such as human milk oligosaccharides in the case of ‘infant type’ bifidobacteria) to support their metabolic activities and persistence in the gut[11,12,13] For this reason the Bifidobacterium pan-genome consists of a relatively high percentage (~13.5%) genes assigned to glycan metabolism[14] and their glycan-degrading capabilities can be further expanded through resource-sharing and cross-feeding strategies involving other members of the gut community[15,16,17]. Based on a comparative and pan-genome analysis conducted on thirteen representatives of the B. breve species, variable genetic features (the variome) were identified that are responsible for strain diversification, including genes involved in host or environment interactions, such as biosynthesis of cell surface-exposed structures www.nature.com/scientificreports/
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