Domesticated animals experienced profound changes in diet, environment, and social interactions that likely shaped their gut microbiota and were potentially analogous to ecological changes experienced by humans during industrialization. Comparing the gut microbiota of wild and domesticated mammals plus chimpanzees and humans, we found a strong signal of domestication in overall gut microbial community composition and similar changes in composition with domestication and industrialization. Reciprocal diet switches within mouse and canid dyads demonstrated the critical role of diet in shaping the domesticated gut microbiota. Notably, we succeeded in recovering wild-like microbiota in domesticated mice through experimental colonization. Although fundamentally different processes, we conclude that domestication and industrialization have impacted the gut microbiota in related ways, likely through shared ecological change. Our findings highlight the utility, and limitations, of domesticated animal models for human research and the importance of studying wild animals and non-industrialized humans for interrogating signals of host–microbial coevolution.

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Domestication may have had convergent effects on the microbiota of domesticates and 15 humans through analogous ecological shifts. Comparing the gut microbiota of domestic and related 16 wild mammals plus humans and chimpanzees, we found consistent shifts in composition in 17 domestic animals and in humans from industrialized but not traditional societies. Reciprocal diet 18 switches in mice and canids demonstrated that diet played a dominant role in shaping the domestic 19 gut microbiota, with stronger responses in the member of the wild-domestic pair with higher 20 dietary and microbial diversity. Laboratory mice recovered wild-like microbial diversity and 21 responsiveness with experimental colonization. We conclude that domestication and 22 65 the average of its host pair along the first and second NMDS axis. Domestic individuals were 66 typically further right (axis 1: P<0.001, Mann-Whitney U test; Fig. 1C) and further up (axis 2: 67 P=0.007; Fig. 1D) relative to the average of their host pair. Domestic species all displayed these 68 shifts, whether classified as laboratory, agricultural, or companion animals (P<0.05, Mann-69

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