Host genetics and environment shape the composition of the gastrointestinal microbiome in nonhuman primates

The bacterial component of the gastrointestinal (GI) tract microbiome is comprised of thousands of species of individual taxa, the vast majority of which live in symbiosis with the host. The composition of the bacterial microbiome is dramatically influenced by host diet and disease history, and host genetics may additionally play a role. To understand the degree to which host genetics can shape the composition of the GI tract microbiome, here we studied fecal microbiomes in 4 species (of 2 genera) of nonhuman primates (NHP) held in facilities at 2 campuses but fed the same base diet. These animals include two species of Asian macaques (Macaca mulatta and Macaca nemestrina) and two species of old-world monkeys of African descent (Chlorocebus sabaeus and Chlorocebus pygerythrus). We also follow the composition of the GI tract microbiome in several NHPs as they transition from an outdoor to an indoor environment and compared outdoor-to-indoor transitioned C. pygerythrus to their captive-born offspring. We find that genetics can influence the composition of the microbiome, with animals of different genera having dramatically different GI tract microbiomes, whereas animals within the same genera (but different species) have similar microbiomes. These data point to the degree to which host genetics can influence the composition of the GI tract microbiome when diet is controlled and suggest, within primate species, individual host genetics are unlikely to alter the microbiome dramatically. These data are important for the development of therapeutics aimed at altering the microbiome in outbred populations of genetically-disparate members of the same species. Contact: Jason Brenchley. This submission was powered by METAGENOTE (https://metagenote.niaid.nih.gov).