The overall goal of research in the Auchtung lab is to understand how the gastrointestinal microbiome contributes to human health and to use this information to develop new microbiome-targeted therapies to treat disease. Currently, our work focuses on how antibiotics disrupt microbiome-mediated resistance to colonization by antibiotic-resistant pathogens. Our primary emphasis is the gastrointestinal pathogen Clostridioides difficile, the leading cause of antibiotic-associated diarrhea and hospital-acquired infections. Our lab examines the impact that interpersonal variation in microbiome composition has on susceptibility to disease and response to potential therapeutics. We use two complimentary approaches to model interpersonal variation, human fecal minibioreactors and humanized microbiota mice. Human fecal minibioreactors are a high-throughput model for culturing complex communities of human intestinal microbes that can be used to study how varying microbe composition, antibiotic treatment, and dietary variation influence microbiome function. We use humanized microbiota mice to test these same influences on microbiome function in the presence of a mammalian host. Identifying mechanisms conserved across these complementary models will provide important insights into how the GI microbiome contributes to health that may translate into new therapies. 

In December 2018, a project in the Auchtung lab was featured in a video:
               How Bacteria Respond to Antibiotics