Quantifying the role of the gut microbiome in host essential amino acid metabolism

Intestinal microbiota perform many functions for their host, but among the most important is their role in metabolism, especially the conversion of recalcitrant biomass that the host is unable to digest into bioavailable compounds. Most studies have focused on the assistance gut microbiota provide in the metabolism of carbohydrates, however, the role they play in the amino acid metabolism of their host is poorly understood. We conducted an experiment on Mus musculus using 16S rRNA sequencing and essential amino acid (AAESS) carbon isotope analysis to quantify the community composition of gut microbiota, and the contribution of carbohydrate carbon used by the gut microbiome to synthesize AAESS assimilated by mice to build skeletal muscle tissue. The relative abundances of Firmicutes and Bacteroidetes inversely varied as a function of dietary macromolecular content, with Firmicutes dominating in low-protein diets that contained the highest proportions of simple carbohydrates (sucrose). Concentration-dependent mixing models estimated that the microbial contribution of AAESS to mouse muscle varied from <5% (threonine, lysine, and phenylalanine) to ~60% (valine) across diet treatments, with the Firmicute dominated microbiome having the greatest contribution. Our results show that intestinal microbes can provide a significant source of essential AAESS their host utilize to synthesize structural tissues. The role that gut microbiota play in the amino acid metabolism of animals that consume protein deficient diets is likely a significant but under-recognized aspect of foraging ecology and physiology.