Alice Risely, Dominik W. Schmid, Nadine Mueller-Klein, Kerstin Wilhelm, Tim Clutton-Brock, Marta B. Manser, Simone Sommer

Inter-individual differences in gut microbiota composition are hypothesized to generate variation in host fitness – a premise for the evolution of host-gut microbe symbioses. However, recent evidence suggests that gut microbial communities are highly dynamic, challenging the notion that individuals harbour unique and stable gut microbial phenotypes. Leveraging a long-term dataset of wild meerkats, we reconcile these concepts by demonstrating that the relative importance of identity to shaping gut microbiota phenotypes compared to social group and annual variation depends on temporal scale. Across meerkat lifespan, annual variation overshadows the effects of identity and social group in predicting gut microbiota composition, with identity explaining on average less than 2% of variation across microbial phenotypes. However, identity is the strongest predictor of microbial phenotypes over shorter time periods, predicting on average 20% of variation before rapidly declining in explanatory power over longer periods. Decomposing drivers of variation highlight that identity, social group, and year are each associated with distinct phylogenetic groups of taxa. The effects of identity are also dependent on meerkat age, with the gut microbiota becoming more individualized and stable as meerkats get older. These findings illuminate the degree to which individualised gut microbial signatures can be expected, with important implications for the time frames over which gut microbial phenotypes may mediate host physiology, behaviour and fitness in natural populations.