Avenues of future research
A major objective for future investigations on the daily rhythms of the gut microbiome is to quantify their prevalence and strength across natural populations. Currently, our knowledge on gut microbial oscillations largely stems from laboratory mice, whilst our understanding of circadian rhythms of wildlife is largely restricted to behaviour 61. To understand the adaptive significance of circadian rhythms and their entrainment by the gut microbiota, we need to move the study of circadian rhythms to natural populations. This is particularly true given the importance of food intake on system-wide circadian rhythms, because feeding times of captive animals generally do not mirror foraging regimes of wild counterparts. As such, whilst studies on captive animals may help disentangle drivers of circadian rhythms, they may not actually reflect circadian rhythms in nature or capture how the interactions between multiple environmental and social cues act to entrain rhythms. Below we briefly outline how integrating gut microbiome and circadian rhythm research in wildlife can advance several outstanding questions in ecology (Fig. 3).