Diet, feeding pattern and host genetics modulate circadian dynamics of the ileal microbiome and transcriptome

Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms. Diet-induced obesity (DIO) perturbs microbial oscillations and causes peripheral circadian disruption. Though time-restricted feeding (TRF) maintains circadian synchrony and protects against DIO, its impact on the dynamics of the distal gut microbiome is modest. Thus, other regions of the gut may play a more important role in entraining peripheral circadian rhythms. Here we demonstrate the effect of diet and feeding rhythms on the ileal microbiome composition and transcriptome in mice. The dynamic rhythms of ileal microbiome composition and transcriptome are greatly impaired in DIO. TRF prevents the effects of a high-fat diet on host ileal microbiome and transcriptome and modulates additional changes that could explain how TRF exerts its metabolic benefits. In addition, the circadian clock is necessary for maintaining ileal microbiome rhythms.