Cohousing or cross-fostering followed by cohousing does not normalize the microbiomes of genetically distinct adult mice

It is widely assumed that the horizontal transmission of microorganisms due to coprophagy or colonization of newborns normalizes the microbiomes of genetically distinct mice. Accordingly, cohousing animals of different genetic backgrounds or fostering them as neonates by the same females is commonly used for equilibrating microbial communities in laboratory mice. To assess whether these assumptions hold true under well-controlled experimental conditions, we analyze the composition of the gut commensal bacteria of adult mice from distinct genetic backgrounds either foster nursed by the same dams or cohoused as adults. Despite shared environmental conditions, significant differences in the gut bacterial profiles idiosyncratic to genetic backgrounds persist across all experiments. These findings indicate that host genetics play a crucial role in maintaining specific microbial communities in adult mice that cannot be permanently altered by either foster nursing or cohousing.