Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.

昼夜节律是使生物功能与昼夜周期同步的内在分子机制。哺乳动物肠道内栖息着无数微生物，统称为肠道微生物群。微生物群通过代谢物和结构成分影响宿主生理机能。一个关键机制是宿主表观遗传途径的调节，尤其是组蛋白修饰。越来越多的研究表明微生物群在调节宿主昼夜节律中的作用。然而，其机制仍然很大程度上未知。在这里，我们总结了微生物调节宿主昼夜节律和表观遗传途径的研究，重点介绍了微生物群如何利用宿主表观遗传机制来调节昼夜节律的最新发现，并讨论了其对宿主生理学，特别是免疫和代谢功能的影响。我们进一步描述了当前的挑战和资源，这些挑战和资源可以促进微生物群-表观遗传-昼夜节律相互作用的研究，以增进我们对昼夜节律紊乱和可能的治疗途径的了解。