Figure 3) The involvement of food intake and gut microbial oscillations in mediating both metabolism and innate immunity raises several questions regarding their function across a range of ecological contexts. The figure visualizes the expected rhythms of mucosal commensals like under six ecological contexts.
Yet, microbiota-independent mechanisms may be expected in species where feeding, metabolic, and immune requirements are uncoupled. For example, ectotherms exhibit circadian rhythms in body temperature and activity62–64, and have some level of circadian cycles in metabolism 65 and immunity 66,67, but feeding patterns are often not circadian (e.g. for large reptiles such as snakes and crocodiles). In these cases, does the gut microbiota undergo diurnal oscillations, and is the entrainment of innate immunity completely independent of the gut microbiota? Given findings from laboratory mice, one might expect that diurnal rhythms of the gut microbiota to be strongest after feeding (Fig. 3). In social or gregarious animals, microbiota are often shared and pathogen exposure increases 68–70, providing another example where pathogen exposure may not be closely correlated with food intake. Therefore, peaks in pathogen exposure or activation of immunity may not be limited to mealtimes. This raises the question as to whether social animals have altered circadian rhythms in immune function compared to solitary species, and whether such adaptations are mediated by the gut microbiota.
Considering microbial rhythms in the context of metabolic and immune requirements throughout the day may provide a useful framework to predict the strength and the functional role of gut microbial oscillations that goes beyond light and temperature cycles. Nevertheless, investigating microbial oscillations across latitudes and in environments with extreme light or temperature conditions (e.g. cave, arctic, or desert animals) will aid our understanding of the circumstances under which microbial rhythms occur. For example, gut microbiome rhythms in meerkats may be particular strong due to the arid environment they inhabit 26, which is characterised by steep temperature differentials between day and night. This extreme fluctuation induces nightly torpor in small desert mammals71, and whilst it is unclear whether meerkats undergo a similar process, it might be expected that extreme temperatures exert metabolic constraints that both influence and are influenced by the gut microbiota.