View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Human commensal gut microbes play a crucial role in host health, including aiding with the digestion of foods that humans cannot digest themselves. Despite the importance of such microbes to human health, there is little knowledge about the evolutionary history of commensal gut microbes, including their demographic histories and how selective forces shape their genetic variation. In this study, we infer the demographic history for the 27 most highly prevalent commensal gut microbial species in North Americans. Several of these species show evidence of population contractions coincident with the onset of agricultural expansion approximately 10,000 years ago. These results are consistent with reductions in diversity observed at the species and genetic level in commensal microbes sampled from Western populations relative to non-Western rural populations with diets consisting of higher amounts of fiber. However, our present results contrast with the population expansions observed in a similar timeframe by the cavity-causing oral microbe, Streptococcus mutans. Taken together, we infer that changes in diet over the course of human history have resulted in effective population size contractions of gut microbiota.

Inference of the demographic history of commensal gut microbes