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Thaiss, et al_2016_Cell_Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

The intestinal microbiota undergoes diurnal compositional
and functional oscillations that affect metabolic
homeostasis, but themechanismsby which the rhythmic
microbiota influences host circadian activity
remain elusive. Using integrated multi-omics and
imaging approaches, we demonstrate that the gut
microbiota features oscillating biogeographical localization
and metabolome patterns that determine the
rhythmic exposure of the intestinal epithelium to
different bacterial species and their metabolites over
the course of a day.

This diurnal microbial behavior
drives, in turn, the global programming of the host
circadian transcriptional, epigenetic, and metabolite
oscillations. Surprisingly, disruption of homeostatic
microbiome rhythmicity not only abrogates normal
chromatin and transcriptional oscillations of the
host, but also incites genome-wide de novo oscillations
in both intestine and liver, thereby impacting
diurnal fluctuations of host physiology and disease
susceptibility. As such, the rhythmic biogeography
andmetabolomeof the intestinal microbiota regulates
the temporal organization and functional outcome of
host transcriptional and epigenetic programs.

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