Animals live in partnership with their gut microbiota, and these microbial communities often shift when hosts adapt to new environments. While it is well known that the microbiome can influence traits ranging from metabolism to behavior, a key question remains unresolved: can host traits under natural selection be transmitted solely through the microbiome, without changes to the host genome? Here we experimentally demonstrate that selection on a behavioral trait in mice significantly shifts the host trait over time through microbiome transmission alone. We first identify locomotor activity as transmissible through the gut microbiome, using fecal transfers from wild-derived mouse strains into germ-free male recipients. Building on this, we carry out four rounds of one-sided microbiome selection, serially transferring microbiomes from low-activity donors to independently bred male germ-free mice. Only this selection line, not the randomly chosen control line, shows a decrease in locomotion toward the end of the experiment. Reduced activity is linked to enrichment of Lactobacillus and its metabolite indolelactic acid, and administration of either alone is sufficient to suppress locomotion. These findings demonstrate that microbiome selection and transmission can shape mammalian behavior, independent of host genomic evolution. Our work highlights the role of microbiome-mediated trait inheritance in shaping host ecology and evolution.
© 2025. The Author(s).