Synchrony and idiosyncrasy in the gut microbiome of wild primates
Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in diets, environments, and medications, but it could also emerge from fundamental ecological forces that shape primate microbiota more generally. Here we leverage extensive gut microbiome time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, we find strong evidence for idiosyncrasy. Over time, samples from the same baboon were much more similar than samples from different baboons, and host-specific factors collectively explained 30% of the deviance in microbiome dynamics, compared to just 3% for factors shared across hosts. Hence, individualization may be common to mammalian gut microbiota, and designing universal microbiome interventions may face challenges beyond heterogeneity in human lifestyles.