The microbiota coordinates diurnal rhythms in innate immunity with the circadian clock

Environmental light cycles entrain circadian feeding behaviors in animals that produce rhythms in exposure to foodborne bacteria. Here, we show that the intestinal microbiota generates diurnal rhythms in innate immunity that synchronize with feeding rhythms to anticipate microbial exposure. Rhythmic expression of antimicrobial proteins was driven by daily rhythms in epithelial attachment by segmented filamentous bacteria (SFB), members of the mouse intestinal microbiota. Rhythmic SFB attachment was driven by the circadian clock through control of feeding rhythms. Mechanistically, rhythmic SFB attachment activated an immunological circuit involving group 3 innate lymphoid cells. This circuit triggered oscillations in epithelial STAT3 expression and activation that produced rhythmic antimicrobial protein expression and caused resistance to Salmonella Typhimurium infection to vary across the day-night cycle. Thus, host feeding rhythms synchronize with the microbiota to promote rhythms in intestinal innate immunity that anticipate exogenous microbial exposure. [Display omitted] •The intestinal microbiota generates daily rhythms in antimicrobial proteins (AMPs)•Rhythmic epithelial attachment of SFB drives rhythms in STAT3 through ILC3•Rhythmic STAT3 expression generates rhythms in AMP expression•Rhythmic AMP production causes day-night variation in resistance to infection Gut microbiota generate circadian rhythms in innate immunity that synchronize with feeding and anticipate exogenous microbial exposure.