The role of diet and host species in shaping the seasonal dynamics of the gut microbiome.

The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.