The microbiome interacts with the circadian clock and dietary composition to regulate metabolite cycling in the gut

The gut microbiome plays a key role in the maintenance of host metabolic homeostasis and health. Most metabolic processes cycle with a 24 hour rhythm, but the extent to which the microbiome influences metabolite cycling under different conditions, such as variations in dietary composition, is largely unknown. In this study, we utilized high temporal resolution metabolite profiling of the Drosophila gut to investigate the role of the microbiome in metabolite cycling. Although the microbiome was previously shown to dampen transcript cycling in the gut, we find that in contrast it increases the number of oscillating metabolites. Interestingly, effects of microbiome loss on metabolite cycling are reduced in a time restricted feeding (TF) paradigm. Conversely, promotion of cycling by TF is reduced in microbiome-containing flies, suggesting that TF compensates for deficits in the microbiome to some extent. In a clock mutant background, loss of the microbiome increases cycling of some classes of metabolites but profoundly affects phase of all of them, indicating the host clock modulates effects of the microbiome on cycling and maintains phase in the face of microbial changes. Lastly, a high protein diet increases microbiome-dependent metabolite cycling but a high sugar diet suppresses such cycling while altering phase. Indeed, we observe that amino acid metabolism is the metabolic pathway most affected by changes in the gut microbiome, the circadian clock and timed feeding. Collectively, our observations highlight a key role of the gut microbiome in contributing to host metabolite cycling, and reveal a complex interaction with internal and external factors. ### Competing Interest Statement The authors have declared no competing interest.