The intestinal microbiota is a fundamental factor that broadly influences physiology. Thus,
studies using transgenic animals should be designed to limit the confounding effects of
microbiota variation between strains. Here, we report the impact on intestinal microbiota of
co-housed versus F2-generation littermates, two commonly used techniques to standardize
microbiota in animal models. Our results establish that while fecal microbiota is partially
normalized by extended co-housing, mucosal communities associated with the proximal …