Figure 2) Diurnal rhythms of the gut microbiota, host
immunity and pathogen abundance across a) the active phase and b) the
rest phase, as characterised in laboratory mice. SFB = Segmented
Filamentous Bacteria.
Interactions between food intake, mucosal commensals, and sIgA together
regulate gut microbial oscillations over the day. However, an additional
mechanism that has received less attention is the role of ecological
dynamics in regulating microbial oscillations. An increase in gut
microbes post-feeding alter the chemistry of the gut, increasing
CO2 and methane levels and decreasing the pH29. Changes to gut conditions after rapid
proliferation of microbes post-feeding may be less favourable for many
microbes, potentially contributing to the consequent reduction in the
bacterial population late in the active phase despite food still being
available and probably ingested. Changes to gut conditions may therefore
reinforce microbial rhythms by ensuring that they are only triggered
once at first food intake after fasting. This pattern is supported by
microbial dynamics in wild meerkats, where bacterial load peaks after
dawn foraging, but not in the late afternoon prior to sunset when
meerkats forage a second time 26.
Whilst we focus here on mechanisms underpinning interactions between gut
bacteria and the innate immune system, gut microbial rhythms also
trigger molecular cascades that regulate metabolism and hormone
production across the day 7,9,14,41,44,60. Circadian
changes to some bacterial metabolites, such as short-chain fatty acids
(SCFAs) and bile acids, are particularly important for upregulating
lipid metabolism and absorption during the active phase7,11. The bacterial compounds lipopolysaccharide (LPS)
and flagellin, which are found in the cell walls of gram-negative
bacteria, have also been implicated in the diurnal dynamics of body
weight and corticosterone synthesis in mice 44.
Notably, these pathways are mediated by the host innate immune system,
with LPS and flagellin being detected by Toll-like receptors
(TLRs)44. The gut microbiota also generate
neuro-active metabolites such as tryptophan and serotonin, therefore
oscillations of the gut microbiota may cause circadian rhythms in
neuro-active compounds that can directly communicate with the nervous
system and influence cognitive processes and stress responses9. However, the link between microbial oscillations
and circadian behaviour remains speculative.