Response of the gut microbiome and metabolome to dietary fiber in healthy dogs

Dietary fiber has been shown to expand beneficial microbial activity in the gut and is being explored to maximize health-related benefits from the microbiome in both humans and companion animals. However, a clear understanding of the precise interactions among fiber-containing diets, specific fibers, and microbiome composition and function is lacking. To fill this knowledge gap, we analyzed fecal metagenomic and metabolomic profiles from 18 healthy dogs at 13 time points each (totaling 226 samples) that were fed 12 test foods containing different fiber sources and quantities (5-13% fiber on an as-fed basis) belonging to three food groups (high starch/low fiber, medium starch/medium fiber, and low starch/high fiber). Taxonomic and functional profiling identified taxa and functions whose abundances were associated either with overall fiber intake or specific fiber compositions. Short-chain fatty acids (SCFAs), acylglycerols, and intermediate products of fiber degradation including sugars (arabinose, xylulose, fucose) and intercalating polyphenols (genistein, hesperidin, limonin, naringenin, and secoisolariciresinol) were enriched in response to intake of insoluble fiber. Some of these were also associated with affected microbes in particular food groups. Eleven species were significantly enriched in response to only one food group. Accordingly, enrichment of beneficial metabolites such as SCFAs was more pronounced in response to these fiber sources, highlighting the importance of interactions between specific dietary components and individual microbes. That is, the production of beneficial metabolites was dependent on both the presence of the appropriate pre-existing microbiota, and the introduction of an appropriate dietary substrate. Correspondingly, the response of microbes to dietary macronutrients varied across subjects, as did the metabolomic consequences of the foods and their overall influence on the microbiome. These data are useful for directing population-wide dietary modifications and for personalized health targeting, with implications for other animals and humans.