In any rapidly changing environment, there are winners and there are losers. The human microbiome—the vast community of microbes that live in and on the human body—is no exception. As scientists gain a deeper understanding of the microbiome’s complex ecology, particularly in the gut, it is increasingly clear that our microbiome’s diversity, globally speaking, is under threat. Spreading industrialization and urbanization, diets dominated by processed foods, industries that promote antibiotic use—all are slashing gut microbe diversity.