Daily light-dark cycles shape the physiology and activity patterns of nearly all organisms. Recent evidence that gut microbial oscillations synchronise circadian rhythms in host immunity and metabolism indicate that diurnal dynamics is a crucial component of microbiome function. However, their prevalence and functional significance are rarely tested in natural populations. Here we summarize the hallmarks of gut microbiota oscillations and the mechanisms by which they synchronise rhythms in host immunity and metabolism. We discuss the consequences for diverse biological processes such as host pathogen susceptibility and seasonal switches in metabolism, and outline how the breakdown of these circadian interactions, for example during senescence and as a consequence of urbanisation, may affect wildlife infection risk and disease. Lastly, we provide practical guidelines for the measurement of microbial oscillations in wildlife, highlighting that whilst wild animals are rarely available over a 24-hour period, characterising even parts of the cycle can be informative. Light-dark cycles are an almost universal environmental cue and provide a rare opportunity to generalise gut microbial responses across species. An improved understanding of how microbial rhythms manifest in wildlife is essential to fully comprehend their ecological significance.