Precision microbiome modulation with discrete dietary fiber structures to direct SCFA production

The gut microbiota is linked to a wide range of pathologies, making it a promising target for improving health. Modulation of the gut microbiota can be achieved by dietary fibers, such as resistant starches, which have demonstrated a role in the prevention of these diseases. However, it is unknown if targeted manipulation of gut microbiota composition, and especially function can be achieved by specific doses of structurally similar yet district fibers. The objective of this study was to compare the effect and dose-response of three different type-4 resistant starches (RS4s) on microbiome composition and function. Using a randomized, double blind, placebo controlled, four arm design, 40 subjects were assigned to consume either one of three RS4s (derived from hi-maize, potato, or tapioca) or a digestible starch for four weeks. The fiber dose was raised each week from 0 to 50 g/d, and fecal samples were collected at the end of each week. Microbiota composition and SCFA were assessed by 16S rRNA gene sequencing and gas chromatography, respectively. Maize and tapioca RS4s, at doses =35 g/d, significantly affected the global composition of the microbiota, decreasing a-diversity and increasing ß-diversity compared to baseline. Interestingly, effects of RS4s on microbiota composition and fecal SCFA were distinct and reflected differences in RS4 structure. Maize RS4 enriched Operational Taxonomic Units related to Eubacterium rectale (OTU1), Ruminococcus spp (OTU27), and Bifidobacterium adolescentis (OTU3), and increased butyrate. Although there was overlap in the enrichment of B. adolescentis, tapioca RS4 enriched Parabacteroides distasonis (OTU21) and Eisenbergiella spp (OTU9) (but not E. rectale or Ruminococcus spp), and increased propionate. These affects were dose-dependent with a plateau at the 35 g/d dose. In contrast, potato RS4 and digestible starch did not significantly modulate the microbiome. These findings provide essential information on how molecular differences in starch structure can result in specific and dose-dependent alterations of the gut microbiome, providing a basis for precision microbiome modulation through nutritional strategies