The intestinal circadian clock drives microbial rhythmicity to maintain gastrointestinal homeostasis

Fecal microbial oscillations are maintained in mice kept in the absence of light, supporting a role of the hosts circadian system rather than representing a diurnal response to environmental changes. Intestinal epithelial cell specific ablation of the core clock gene Bmal1 disrupts rhythmicity of microbiota. Targeted metabolomics functionally link intestinal clock controlled bacteria to microbial derived products, in particular branched chain fatty acids and secondary bile acids. Microbiota transfer from intestinal clock deficient mice into germfree mice altered intestinal gene expression, enhanced lymphoid organ weights and suppressed immune cell recruitment. These results highlight the importance of functional intestinal clocks for circadian microbiota composition and function, which is required to balance the hosts gastrointestinal homeostasis.