Basic Biology of Rhythms and the Microbiome

The mammalian microbiome undergoes diurnal oscillations in composition and function throughout a 24-period that are regulated by host clock and nutritional signals. These diurnal oscillations, in turn, impact the host’s transcriptome and multiple other physiologic functions. Emerging evidence has begun to uncover the molecular mechanisms that underlie the coordinated meta-organismal diurnal rhythmicity with crucial implications for homeostasis and disease. Herein, we highlight current mechanistic understanding by which the diurnally oscillating commensal microbiota is regulated by the host and its environment, and how commensals diurnally modulate host biology in health and disease. Finally, current challenges, open questions, and perspectives in this exciting new field of chronobiology are discussed.