Culture-independent profiling of the stool microbiome identifies bacteria associated with diarrheal disease outbreak in an immunocompromised mouse colony

We have described a diarrheal disease outbreak that occurred at a University of Pennsylvania Laboratory Animal Resource facility in 2015. Using next-generation sequencing technologies to profile the stool microbiome, we identified putative culprits and based on the total histology, necropsy, and DNA results, husbandry changes were made to this facility to prevent such an outbreak from occurring in the future. We believe that this work will be of interest to the broader laboratory animal research community for both outbreak prevention and utilizing DNA sequencing technologies and bioinformatics tools for rapid identification of pathogens in animal research facilities.