3) Interactions between circadian and seasonal rhythms
Seasonal shifts in gut microbiome composition and function have been well described 78–83, but emerging evidence suggests that changes to function may be mediated via increasing or decreasing the amplitude of host circadian rhythms 76. In giant pandas, seasonal switching of diet from bamboo leaves to shoots causes an increase in the bacterial metabolite butyrate in the gut microbiota, and when transferred to mice, this causes the upregulation of clock genePer2, which increases lipid production and fat deposition in spring 76. This study does not measure gut microbial oscillations directly however, and it is unclear whether microbial rhythms also increase in amplitude during spring. Yet, the findings suggest that seasonal cycling of the gut microbiota functions via interacting with host circadian rhythms.
In addition to seasonal diet switches, seasonal changes to life history stages that involve metabolic restructuring such as migration, hibernation, and even reproduction may also be paired with changes to the amplitude of their gut microbial rhythms (Fig. 3). Shifts in the gut microbiota during hibernation adaptively lower metabolism and recycle nitrogen 84–86, yet it remains unknown how these functional changes interact with or are mediated by diurnal rhythms. Seasonal switches in strategies may take more unpredictable and fascinating forms. For instance, the circadian rhythms of some arctic-breeding shorebirds become uncoupled from environmental cues during breeding due to pressures of incubation and predators, with social cues becoming the dominant form of entrainment87. How might such changes be reflected in the gut microbiome?