Bifidobacterium-host-diet interactions

Bacteria belonging to the genus Bifidobacterium are key members of the gut microbiota. They are widely distributed in the animal kingdom, with over 80 recognised species and subspecies, and a host range spanning from insects to mammals. Bifidobacterium are among the earliest colonisers of the human gastrointestinal tract and have been associated with health-promoting benefits. However, investigations of infant-associated Bifidobacterium across early-life changing dietary periods are lacking. In addition, there is limited information on the diversity and the saccharolytic properties of this important microbiota member in diverse animal hosts. Thus, in this work I sought to comprehensively explore human- and animal-associated Bifidobacterium strains using both genomic and phenotypic approaches. Whole genome sequencing (WGS) and bioinformatic analyses were employed to examine a unique collection of Bifidobacterium longum strains (n=75) isolated from nine either exclusively breast- or formula-fed infants across their first 18 months, encompassing pre-weaning, weaning and post-weaning dietary stages, as well as a novel collection of animal-associated Bifidobacterium isolates and publicly available sequences recovered from a diverse range of hosts (n=433). These genomes were analysed either in combination or as discrete subsets to determine their genomic diversity and predicted functional properties related to carbohydrate metabolism. To complement bioinformatic analyses, a subset of infant-associated B. longum isolates were characterised phenotypically using experimental approaches to determine their carbohydrate metabolism capabilities, which linked to genomic analysis. Glycan uptake analysis and proteomics resulted in the determination of the mechanisms employed by selected B. longum strains to metabolise different carbohydrates. Bacterial isolation resulted in the recovery of a substantial collection of animal-associated Bifidobacterium isolates (over 100) and the identification of potential novel species. The results of the bioinformatic analysis indicated a highly diverse “open” pan-genome and an overall very broad repertoire of carbohydrate utilisation genes that could be associated with the host diet. This work represents the largest phylogenetic and comparative genomic analysis of animal-associated Bifidobacterium isolates to date. Overall, this work enhances our current understanding of genomic and phenotypic properties of Bifidobacterium and lays the foundation for subsequent in-depth research aiming at further assessment of animal and human-associated Bifidobacterium diversity, and their functional potential for both therapeutic and industrial applications