Integrative genomic reconstruction of carbohydrate utilization networks in bifidobacteria: global trends, local variability, and dietary adaptation

ABSTRACT: Bifidobacteria are among the earliest colonizers of the human gut, conferring numerous health benefits. While various Bifidobacterium strains are used as probiotics, individual responses to probiotic supplementation may vary due to strain type(s), gut community composition, diet, and health or lifestyle conditions. Given the saccharolytic nature of bifidobacteria, a comprehensive understanding of their glycan metabolism at the strain level is necessary to rationally design probiotic and synbiotic formulations. In this study, we systematically reconstructed 68 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the representation of 589 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 3083 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs) of human origin. Our analysis uncovered extensive inter- and intraspecies heterogeneity, including a yet undescribed phenotypically distinct subspecies-level clade within the Bifidobacterium longum species. We also identified Bangladeshi isolates harboring unique gene clusters tentatively implicated in the breakdown of xyloglucan and human milk oligosaccharides. Thirty-eight predicted carbohydrate utilization phenotypes were experimentally validated in 30 geographically diverse Bifidobacterium isolates. Our large-scale genomic compendium considerably expands the knowledge of bifidobacterial carbohydrate metabolism, providing a foundation for the rational design of probiotic and synbiotic formulations tailored to strain-specific nutrient preferences.

ORGANISM(S): Bifidobacterium catenulatum subsp. kashiwanohense

PROVIDER: GSE239955 | GEO | 2024/08/08

REPOSITORIES: GEO