Mouse microbiome associated with housing status and viral exposure

The bacterial microbiome has a major impact on health and can shape metabolism, host-tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen free animals have reduced microbiome diversity, making it difficult to evaluate the impact of infection-induced microbiome disruption that would be observed in free living animals, including people. Mice are commonly used as a preclinical model but unfortunately often fail to predict translation success or failure, particularly for immune and infectious disease targeting therapies. Here, we compare how pet store mouse cohousing to generate 'dirty' mice differentially affects the airway and gastrointestinal microbiomes at baseline and during acute respiratory influenza A virus infection.