Studying gut microbial rhythms in wildlife
Field ecologists face a number of challenges that may have acted to delay the integration of circadian rhythms into field ecology, such as limited availability of study animals across a 24-hour period. However, as long as individuals can be sampled over the morning and preferably also the afternoon (e.g. 26) then many questions on microbial oscillations can be tackled. Indeed, the period after the start of the active phase is often when the largest changes occur and therefore reporting just this part of the diurnal cycle is informative. Whilst a longitudinal study design is preferable, the strength of microbial oscillations reported so far suggest that cross-sectional study designs may also have sufficient statistical power to detect predictable microbial oscillations. For example, in meerkats, sensitivity analyses that restricted analysis to only 20 (cross-sectional) samples per hour during daylight hours (total n ≈ 240) still detected the same microbial oscillations reported with the full dataset (total n ≈1100) 26.
A common obstacle in identifying meaningful associations between the gut microbiota and host physiology is the sheer diversity of gut microbial communities and available physiological markers. Future studies on non-model organisms may therefore benefit from focusing on the key taxa and physiological markers identified from experimental studies to date. Findings from mice indicate that mucosal-associated commensals, in particular SFBs which are found across vertebrates122, play a fundamental role in mediating physiological homeostasis and immunomodulation by attaching to the intestinal epithelium at the start of the active phase. The identity and oscillations of these specific commensals are therefore likely to be disproportionally important for identifying associations between the gut microbiota and host physiology in natural populations. In addition, gut sIgA and antimicrobial peptides (AMPs) are two facets of immunity that have been strongly implicated in circadian interactions with the gut microbiota, whilst the microbial metabolites butyrate, flagellin, and LPS have been implicated in circadian interactions that regulate metabolic signalling pathways. Applying these physiological markers may therefore be particularly suitable for determining whether mechanisms identified in laboratory systems have broad biological relevance for natural populations.