Subtle diurnal microbial rhythms in a large mammalian carnivore

Abstract

Mounting evidence suggests that the cyclic interaction between host cells and the gut microbiota orchestrates metabolic and immunological homeostasis throughout the day. Yet, examples of gut microbial rhythms in natural populations are scarce, limiting our understanding of their downstream consequences for host health, particularly in mammals that demonstrate strong co-evolutionary links with their microbiota. Furthermore, disregarding diurnal microbial variation restricts our ability to account and control for them in future studies. Here, we re-analyzed gut microbiota data from a 23-year longitudinal field study of 12 wild adult female spotted hyenas (Crocuta crocuta) in the Masai Mara National Reserve in Kenya to examine whether time of day was correlated with variation in gut microbial composition in this crepuscular–nocturnal carnivore. Overall, we found that gut microbial composition and structure, but not alpha diversity, slightly changed over the course of the day. Differences in microbiota composition between morning and afternoon became particularly apparent when restricting the analysis to the core microbiota (i.e., bacterial genera present in more than 85% of samples). Among the core microbiota, 11 genera—composed largely of the bacterial class Clostridia—varied in abundance with time of day, making this the second study to document gut microbial rhythms in a longitudinally sampled wildlife population. In contrast with the diurnal gut microbial oscillations of wild meerkats, those of hyenas are subtle, yet both species exhibit shifts specifically in the bacterial class Clostridia. This pattern implies that diurnal fluctuations are likely a characteristic of specific, common host-associated bacteria and their amplitude may be a product of host ecology. While our study detected diurnal trends, we encourage studies to employ a temporally denser sampling scheme. In this way, one can overlay short-term oscillations of the microbiome with information on host ecology and clarify consequences for the circadian phenotype of the host.