Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

Gut microbiota metabolites may be important for host health, yet few studies investigate the correlation between human gut microbiome and production of fecal metabolites and their impact on the plasma metabolome. Since gut microbiota metabolites are influenced by diet, we performed a longitudinal analysis of the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome, including after a microbiota depletion intervention. Omnivore and vegan, but not EEN, diets altered fecal amino acid levels by supporting the growth of Firmicutes capable of amino acid metabolism. This correlated with relative abundance of a sizable number of fecal amino acid metabolites, some not previously associated with the gut microbiota. The effect on the plasma metabolome, in contrast, were modest. The impact of diet, particularly fiber, on the human microbiome influences broad classes of metabolites that may modify health. [Display omitted] •The gut microbiome on a fiber-free diet differs from that of an omnivore or vegan•The lack of dietary fiber slows microbiome recovery after an ecological stress•Dietary effects on Firmicutes alter carbohydrate and amino acid gut metabolites•The effect of diet-based microbiota metabolites on the plasma metabolome is modest Tanes et al. show that consumption of a fiber-free diet shifts the human gut microbiome toward metabolism of simple carbohydrates. Following an ecological stress, omnivore and vegan diets, but not the fiber-free diet, support growth of Firmicutes capable of carbohydrate and amino acid metabolism, altering fecal amino acid level.