Domestication is an evolutionary process which resulted in substantial genetic and ecological changes with potentially profound implications for the microbiota. The domestic microbiota may be predicted to resemble that of industrialized human populations as the disruptions to historic host-microbe relationships were similar—including diet shifts, changes in movement and density, antibiotic use, and altered breeding and birthing. Microbial changes may not have been exclusively negative, however, and if microbial responses to domestication enhanced host phenotypes valuable to humans (e.g., body size or composition, behavior), they may even have been selected for. Here, we sought to document the effects of domestication on the mammalian gut microbiota and determine the forces which distinguish it from the wild microbiota. We first characterized the fecal microbiota of wild and domestic populations of ten pairs of artiodactyl, carnivore, lagomorph, and rodent species using 16s rRNA gene sequencing. To determine the relative importance of environment and genetics, we also performed diet manipulation experiments with captive populations of lab/wild mice and dog/wolves.
Results/Conclusions
Surveying the fecal microbiota across mammalian species pairs, we found consistent differences in the beta-diversity of domestic microbiota although there was no evidence for a convergent domestic microbiota or a predictable effect of domestication on microbial alpha-diversity. In mice, we were able to overcome the differences between wild/domestic genotypes by switching wild mice to a laboratory chow diet. In laboratory mice, colonization with a wild microbiota was more successful than a diet switch alone though, indicating that some wild-associated strains may have been lost during the process of laboratory domestication. In contrast, the dog microbiota was much more responsive to diet shifts than the wolf microbiota. Dogs likely gained new commensal microbes in response to greater omnivory and overall complexity of the domestic diet. Altogether, our data indicate that domestication has had significant effects on the microbiota, at least in part due to dietary and environmental shifts. Associated functional changes may have been the target of anthropogenic selection and, more broadly, illustrate a potential role for microbial shifts in host evolution.