Heritability Of The Gut Microbiome In Wild Baboons (Papio Cynocephalus)

Variation in gut microbiome composition is linked to key health outcomes across primates, and is driven by both environmental and host genetic effects. However, it is often difficult to disentangle genetic from environmental effects because relatives often use the same resources and have similar diets. Moreover, it is difficult to account for long‐term changes in microbiome composition since longitudinal profiles are rarely available. Here, we quantified the heritability of the microbiome using an unprecedented dataset of 16,234 microbiome profiles collected over 14 years from a longitudinally studied population of wild baboons (Papio cynocephalus) with available host genetic relatedness data and rich environmental metadata. We identified heritable microbes while controlling for non‐genetic effects by including granular metadata on host diet, social group, and weather. We found that >95% (98/102) of the analyzed taxa are significantly heritable, although heritability is generally low, and host genetics accounts for 11‐21% of the variation in the abundances of the 15 most heritable taxa. These taxa include Christensenellaceae and Rikenellaceae, bacterial families that are also heritable in humans, suggesting that common host genetic mechanisms may control microbiome composition across primates. Finally, the relative abundance of heritable taxa changes over time within individuals, leading to temporal variation in estimated heritability. This emphasizes the importance of longitudinal studies to account for temporal and environmental effects in shaping gut microbial composition.