September 2021

Abstract:
Coevolution of humans with gut bacteria requires a shared evolutionary history. Host-microbial cophylogeny has been shown for hominids, but within humans, only the stomach bacterium Helicobacter pylori is known to have codiversified with its host. Human populations are known to harbor distinct strains of bacterial species and this is generally attributed to differences in environment and diet, however, codiversification through long-term associations could also contribute to these patterns. To test for cophylogeny between gut microbiota and their human hosts, we analyzed paired human genotypes and bacterial strain genotypes from fecal metagenomes obtained from five countries. Our results indicate that strains of common gut bacteria have transmitted vertically for thousands of generations. In accord, strains displaying patterns of cophylogeny are also shared between mothers and infants. Patterns of strain transfer between populations are consistent with an African origin for taxa showing cophylogeny. Our results indicate long-term fidelity of gut microbial strains with human populations, creating opportunities for coevolution.