Gene–Phenotype Associations Involving Human-Residential Bifidobacteria (HRB) Reveal Significant Species- and Strain-Specificity in Carbohydrate Catabolism

Abstract

Bifidobacteria are among the first colonizers of the human gastrointestinal tract. Different bacterial species use different mechanisms for utilization of various carbon sources in order to establish themselves in the complex microbial ecosystem of the gut. However, these mechanisms still need to be explored. Here, a large gene–phenotype correlation analysis was carried out to explore the metabolic and genetic diversity of bifidobacterial carbohydrate utilization abilities. In this study, we used 21 different carbohydrates to determine the growth phenotypes, the distribution of glycoside hydrolases (GHs), and gene clusters related to the utilization of multiple carbon sources in six human-residential Bifidobacterium species. Five carbohydrates significantly stimulated growth of almost all strains, while the remaining sugars exhibited species- and strain-specificity. Correspondingly, different Bifidobacterium species also had specific GHs involved in fermentation of plant or host glycans. Moreover, we analyzed several carbohydrate utilization gene clusters, such as 2-fucosyllactose (2′FL), sialic acid (SA), and fructooligosaccharide (FOS). In summary, by using 217 bifidobacterial strains and a wide range of growth substrates, our research revealed inter- and intra-species differences in bifidobacterial in terms of carbohydrate utilization. The findings of this study are useful for the process of developing prebiotics for optimum growth of probiotics, especially Bifidobacterium species.

Population-level variation in gut bifidobacterial composition and association with geography, age, ethnicity, and staple food

“…The B. adolescentis isolates had a higher number of glycosidases types and genes encoding glycosidases than the B. pseudocatenulatum isolates, indicating a higher capacity of carbohydrate catabolism. This is in line with previous literature 29 . We identified 16 glycosidase genes with differential gene counts between the two species ( p .adj < 0.05, Mann–Whitney test, Fig.…”

Uncovering the specificity and predictability of tryptophan metabolism in lactic acid bacteria with genomics and metabolomics

“…However, currently known LAB that can metabolize tryptophan are mainly Limosilactobacillus reuteri , and the metabolic ability of other species is unclear. Previous studies have shown that Bifidobacterium of the same species but from different sources have different abilities to use carbon sources ( Liu et al., 2021 ). Therefore, it is also necessary to investigate whether the isolation source has an impact on the LAB’ capacity to metabolize tryptophan.…”

Potential of Inulin-Fructooligosaccharides Extract Produced from Red Onion (Allium cepa var. viviparum (Metz) Mansf.) as an Alternative Prebiotic Product

“…On the other hand, Bb. breve exhibited even greater merit due to the presence of four type-gene clusters associated with FOSs degradation, including β-fructofuranosidase-encoding gene [25]. Thus, it can be implied that Bb.…”