Daily light-dark cycles shape the activity patterns and physiology of nearly all organisms. Many biological processes undergo circadian rhythms, yet rhythms in immunity and metabolism are particularly important for the maintenance of biological homeostasis. Recent evidence that food intake and the gut bacterial microbiota synchronise system-wide circadian rhythms spanning immunity, metabolism, and behaviour point towards gut microbial oscillations being a crucial component of microbiome function. Findings from model systems suggest that gut microbial oscillations are likely widespread across species and pivotal for shaping immune and metabolic responses, yet their prevalence and functional significance are rarely tested in natural populations. Here we summarize results from experimental studies on how circadian interactions between the gut microbiota and the host act to synchronise rhythms in host metabolism and immunity. We outline how these circadian interactions are likely to mediate diverse biological processes, including host pathogen susceptibility and seasonal switches in metabolism, and discuss how the breakdown of these interactions, for example during senescence and urbanisation, can lead to dysbiosis and declines in health. 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 that provide a rare opportunity to generalise gut microbial responses across species, yet to fully appreciate their ecological relevance an understanding of how microbial rhythms manifest in wildlife is essential.