Fiber supplementation influences the phylogenetic structure and functional capacity of the adult human intestinal microbiome

The impact of diet on the composition and functional capacity of the human gastrointestinal microbiome remains under-investigated. We aimed to determine the impact of polydextrose (PDX) and soluble corn fiber (SCF) on the fecal microbiome using shotgun sequencing. Healthy adult males (n=21) were enrolled in a randomized, double-blind, placebo-controlled crossover trial. Subjects consumed 3 treatments (snack bars) containing either no supplemental fiber (NFC), PDX (21 g/d), or SCF (21 g/d) for 21 days. Three fecal samples were collected on days 16-21 of each period; DNA was extracted, followed by shotgun 454 pyrosequencing and analysis using QIIME. UniFrac-based PCoA demonstrated shifts in the phylogenetic structure and functional capacity of the microbiome of subjects consuming fibers compared to controls. Consumption of PDX and SCF resulted in significant (p<0.001) changes in microbial populations at several taxonomic levels, including a shift in the Firmicutes:Bacteroidetes ratio. Functional categories affected by fiber supplementation were associated with carbohydrate, amino acid, and lipid metabolism; metabolism of cofactors and vitamins; mineral and organic ion transport systems; and DNA metabolism. These novel findings demonstrate that fiber supplementation impacts both the phylogenetic structure and functional capacity of the fecal microbiome in adult humans.