Limited codiversification of the gut microbiota within humans

Gut bacteria exhibit striking variation across different human populations, but the evolutionary forces that have shaped this diversity are less well understood. Recent work has argued that many species of gut bacteria have codiversified with modern humans, based on the phylogenetic correlations between human and microbial genomes. Here, I re-analyze these data and show that the correlations between human and microbial phylogenies are often substantially weaker than those between unlinked human chromosomes and that similar correlations can arise through geographic structure alone. These results suggest that traditional codiversification has been limited in recent human history and highlight alternative strategies for quantifying the extent of human-microbe coevolution.

There is widespread interest in understanding the evolutionary history of our gut microbiota and how it varies within and among different human population groups. This Observation critically re-examines the hypothesis that many commensal gut bacteria have evolved in parallel (or "codiversified") with modern humans, providing new evidence that the correlations between human and microbial genealogies are weaker than previously supposed. These findings have important evolutionary implications and also practical consequences, from the sourcing of probiotic therapies to the design of sequencing-based diagnostics.