Bifidobacterium breve UCC2003 exopolysaccharide modulates the early life microbiota by acting as a dietary substrate

Members of the genus Bifidobacterium represent an important bacterial group for promoting health during early life. Previous studies have indicated that bifidobacterial exopolysaccharides (EPS) are involved in host interactions, with purified EPS also suggested to modulate microbe-microbe interactions by acting as a nutrient substrate. To further explore the role of EPS as a potential dietary component, we determined the longitudinal effects of bifidobacterial EPS on microbial communities and metabolite profiles using an infant model colon system. Bifidobacterium breve UCC2003 was utilised as a representative early life bifidobacterial strain, and a corresponding isogenic EPS-deletion mutant (B. breve UCC2003 EPS-). Initial transcriptomics analysis of the EPS mutant vs. parent B. breve UCC2003 strain highlighted differential expression in a discrete number of genes, including the eps biosynthetic cluster, though overall growth dynamics between the two strains were unaffected. Model colon vessels were inoculated with B. breve strains and microbiome dynamics were monitored using metataxonomic (via 16S rRNA sequencing) and metabolomic (via 1H NMR) approaches. Baseline early life microbiota profiles were similar between vessels, with persistence of B. breve (EPS+ and EPS-) observed between 0-36h. Within the EPS-positive vessel there was a significant shift in microbiome and metabolite profiles until the end of the study (405h); we observed increases of Escherichia and Tyzzerella, and short-chain fatty acids including acetate, propionate and formate, including further correlations between taxa and metabolites which were not observed in the EPS-negative vessel. These data indicate that the B. breve UCC2003 EPS is potentially being metabolised by members of the infant microbial community, leading to differential microbial metabolism and altered metabolite by-products. Overall, these findings may allow for development of EPS-specific strategies to beneficially alter the early life microbiota to promote infant health.