Experimental evolution of a mammalian holobiont: selection for herbivorous capability in bank voles yields distinct and robust gut microbial communities

Background Symbiotic associations between animals and their microbiota are increasingly recognized as critical to the functioning of individuals and the evolution of complex adaptations, such as mammalian herbivory. This has led to the development of the "hologenome" theory of evolution, which proposes that natural selection and evolution can act through a conglomerate biological unit, the "holobiont" - the host and its associated microbiome. Although the concept is appealing, its merits are debated, and few attempts have been made to test its specific assumptions directly using the experimental evolutionary approach. Results Here, we fill this gap using lines of bank vole ( Myodes = Clethrionomys glareolus ) selected for enhanced ability to cope with a low-quality herbivorous diet and unselected control lines. In a 4-day test with the low-quality diet, juvenile voles from the "herbivorous" lines maintained or increased body mass better than those from the control lines and had an increased rate of food consumption. Results from a complex nature-nurture design, in which we combined dietary treatment with cohabitation between individuals from the distinct lines (to allow for horizontal bacterial transfer), showed that the "herbivorous" voles harbored a caecal microbiome with altered composition and structure, and altered abundances of several phyla and genera, regardless of the origin of the cohabitant. Although the differences were small, they were partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Conclusions These results, combined with those of a complementary cross-fostering experiment, showed that microbial composition can be treated as an organismal functional trait, largely determined by genetic background and early maternal effects, which can change in response to selection acting on other organismal traits. Such results are consistent with the concept of hologenomic evolution.