The microbiome stabilizes circadian rhythms in the gut

The ways in which the gut microbiome modulates host physiology are of interest from scientific and clinical perspectives. Given that much of physiology is under circadian regulation, we used a Drosophila model to ask how the microbiome interacts with circadian rhythms in the gut. We found that the microbiome itself did not cycle in flies fed ad libitum. A timed feeding (TF) paradigm induced oscillations of some species in clockless per01 flies but effects were small and this paradigm did not detectably enhance fitness. Despite limited circadian, TF and the presence of a microbiome influenced the composition of the gut circadian transcriptome, independently and in concert. In addition, TF altered the phase and amplitude of rhythmic gene expression, with the latter mediated, at least in part, by widespread changes in histone acetylation. Loss of the microbiome increased cycling amplitude in germ-free animals. However, despite their higher amplitude circadian cycling, germ-free flies reset more rapidly following a circadian disruption paradigm. We propose that the microbiome stabilizes cycling in the host gut to prevent rapid fluctuations under different environmental conditions.