Uniform bacterial genetic diversity along the gut.

While environmental gradients are known to result in heterogeneous distributions of bacterial species along the gastrointestinal tract, the spatial distribution of genetic diversity within these species remains poorly understood. Because bacterial genetic variants influence host traits like inflammation and metabolism, understanding their distribution is critical. Here, we analyze ~30 common gut commensals in germ-free mice colonized with the same healthy human stool. Unexpectedly, we find that while species composition varied significantly across gut regions, genetic diversity within species remained remarkably uniform. This uniformity is driven by similar strain frequencies along the gut lumen, indicating that genetically divergent strains can coexist without spatial segregation. Furthermore, ~60 evolutionary adaptations arising within the mice tend to sweep globally throughout the gut, showing little region-specificity. We observe similar dynamics in conventional mice and humans, suggesting that uniform bacterial genetic diversity is a conserved, robust feature of mammalian gut ecosystems.