The degradation of complex polysaccharides from dietary fiber by the gut microbiota produces metabolites, some of which are utilized by the host and can impact immune function. However, few studies have investigated the correlation between the human gut microbiome and production of fecal metabolites and their impact on the plasma metabolome. We performed a longitudinal analysis of a controlled feeding study that included three divergent diets – vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber – as well as a microbiota depletion event. Prior to the microbiota depletion event, the fiber-free EEN diet altered the composition of the gut microbiota which corresponded to a shift towards the metabolism of simple carbohydrates as opposed to complex plant glycans. Following the microbiota depletion event, the omnivore and vegan diets, but not the fiber-free EEN diet, supported the growth of Firmicutes capable of carbohydrate and amino acid metabolism. This correlated with the relative abundance of a sizable number of fecal amino acid metabolites, some of which have not previously been associated with the gut microbiota. Meanwhile, the effect on the plasma metabolome was modest.

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

ACS Fall 2021

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