Prebiotic carbohydrate intake drives changes in bacterial and fungal richness, inter-Domain microbial interactions, and select Bifidobacterium lineages in healthy human subjects. Effect of prebiotic carbohydrates on bacterial and fungal human gut microbiome

Abstract: How diets containing different carbohydrates with prebiotic potential might affect the bacterial, archaeal, and fungal communities of the gut microbiome, as well as the inter-Domain interactions implicit with such diets, are virtually unexplored. Here, we have used single-blinded, randomized crossover study to reveal how gut microbiome of healthy subjects is affected by a diet comprised of foods providing low or moderate amount of prebiotic substrates. 18 healthy adult subjects were randomised and blinded to consume diets prepared to provide either a low (LP 1-3 g/day oligosaccharides; 0.50 g/day polyols) or moderate (MP 6-8 g/day oligosaccharides; 3.66 g/day polyols) prebiotic content. After one-week washout period, the subjects were then crossed over to second diet. Stool samples were collected at the end of each 3-week dietary period, and extracted DNA used for 16S rRNA (Bacteria/Archaea) and ITS2 (Fungi) amplicon-based profiling. In parallel, shotgun metagenomics sequencing was used to produce both higher resolution taxonomy and functional-based assessment of communities, including the production of metagenome assembled genomes. Results: The amplicon-based profiling showed that consumption of MP diet resulted in significant increase of Bifidobacteria and reduced bacterial richness, whereas fungal richness was increased in response to MP diet. Functional (MGS) data revealed genes for starch and polyol utilization were increased in bacterial communities following consumption of MP diet, and that the expansion of Bifidobacterium metabolic niche was attributable to polyol-utilizing B. longum and B. adolescentis. Distinct and novel inter-Domain networks among bacteria, fungi, and archaea were also evident with both diets. Conclusions: Polyols appear to be first rate-limiting nutrient for the growth of select Bifidobacterium spp. offering strategies to restore these populations in a predictable way. Prebiotic intake via natural foods not only affects key Bifidobacterium spp., but also appears to influence fungal richness and drive specific inter-Domain microbial relationships.