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.