Every mammal hosts a hidden community of other organisms—the microbiome. Their intestines teem with complex microbial populations that are critical for nutrition, fighting disease and degrading harmful toxins. Throughout their lives, mammals are exposed to countless microbes through their food and environment, but only a small subset take up permanent residence in the host. Although scientists agree that diet, geography and evolutionary history structure the microbiome, the relative influence of each factor is a mystery. No rigorous study has investigated all three at once in wild mammal populations. Until now.