Gut metagenome in murine colon

Compartmentalization of the gut microbiota into spatially-distinct communities has been suggested to be important in mediating interactions and ecosystem function.Here, by comprehensive spatial sampling of the colonic microbiota with laser capture microdissection and modeling of microbiota variation along longitudinal and lateral axes, we show that there is fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity. This structuring is perturbed in polysaccharide- and fiber-deficient diets.This high-resolution approach has the potential to improve our understanding of the importance of spatial structuring in microbiota function and host–microbiota interactions.