Cage environment regulates gut microbiota independent of toll-like receptors
The gut microbiome orchestrates epithelial homeostasis and both local and remote immunological responses. Critical to these regulatory interactions are innate immune receptors termed toll-like receptors. Studies to date have implicated innate immunity and toll-like receptors in shaping key features of the gut microbiome. However, a variety of biological and environmental variables are also implicated in determining gut microbiota composition. In this report, we hypothesized that co-housing and environment dominated the regulation of gut microbiota in animal models independent of innate immunity. To determine the importance of these variables, innate immunity or environment in shaping gut microbiota, we used a randomized co-housing strategy and transgenic TLR-deficient mice. We have found that mice co-housed together by genotype exhibited limited changes over time in the composition of gut microbiota. However, in mice randomized to cage, we report extensive changes in gut microbiota, independent of TLR function whereby the fecal microbiota of TLR-deficient mice converge with wild type. TLR5-deficient mice in these experiments exhibit a greater susceptibility for comparative changes in microbiota to other TLR-deficient mice and wild type mice. Our work has broad implications for the study of innate immunity and host-microbiota interactions. Given the profound impact that gut dysbiosis may have on immunity, this report highlights the potential impact of co-housing on gut microbiota and indices of inflammation as outcomes in biological models of infectious or inflammatory disease.