Areas of research


Inflammatory Bowel Disease

Inflammatory Bowel Diseases (IBD) are conditions characterized by inflammation that may occur throughout all, or parts, of the digestive tract. There are two main types of IBD, ulcerative colitis and Crohn’s disease, each with very different pathologies. Despite these differences, susceptibility of both diseases is believed to be caused by changes in the microbiome. These changes are due to an individual’s genetics, or through environmental exposures, such as pollutants, prescription drugs, chronic inflammation and diet. Shifts in the microbiome cause an upregulation and activation of mucosal immune and inflammatory pathways without sufficient regulatory responses. The major focus of CMiST will be the multi-disciplinary study of mechanisms leading to chronic intestinal inflammation, identification of interactions between environmental factors and different genetic loci with the microbiome, and the exploration of potential of microbiome-based therapies for these complex inflammatory conditions. We believe that successful therapeutic interventions will require a holistic approach that takes into account the molecular pathophysiology of IBD, specific clinical parameters and both immune and nutritional status.

Diseases studied: Adult & pediatric IBD


Synthetic Biology & Therapeutics

A decade of research has emphasized the importance of the microbiome on human health and disease. Capitalizing on this interaction, recent efforts have sought to create microbiome-based therapeutics using fecal microbiota transplants, probiotics, elimination strategies or prebiotics. However, new approaches to microbiome-based therapies and a more detailed and mechanistic examination of newer technologies such as recombinant probiotics, designed microbial communities and selective antimicrobials must be performed. Further, to effectively translate this work into the clinic, there are numerous challenges that must be understood and the development of microbiome therapeutics have yet to be tested in a comprehensive
fashion. Fundamental understanding of the forces that shape host-associated microbial communities and mediate host-bacterial interactions is essential for the rational design of microbiome therapeutics.

Diseases studied: IBD, HIV/AIDS, infectious disease


Molecular Nutrition & Metabolism

The interactions of nutrition and the microbiome
are highly complex. This is due to the plasticity and diversity of the microbiota within, and across, individuals but also the highly influential nature of diet on the microbiome. The microbiome provides mechanisms that aid in energy recovery through the breakdown of poorly digestible nutrients, such as starch and other polysaccharides. This symbiotic activity influences host metabolism and gene expression. Therefore, application of new strategies to understand how dietary factors impact microbial and host metabolism are key to unlocking the potential for therapeutic discovery.

Diseases studied: Pediatric & adult Non-alcoholic fatty liver disease (NAFLD), irritable
bowel syndrome (IBS), diverticulitis, IBD, infectious disease


Vivo Art

Art and science are more similar than one may think. Deep down both scientists and artists seek to answer the same big questions about life, why are we here, who are we? They both thrive on new innovations and technologies that help them to disassemble aspects of human life in order to discover the building blocks that are necessary for life. Despite these commonalities artists and scientists rarely come together to share their experiences. CMiST will provide support and promote cross-disciplinary approaches and interactions between UW scientists and artists in an effort to cultivate the growth of partnerships between art and science with the goal of educating the UW and greater community regarding the importance of the microbiome and nutrition to health.

Diseases studied: Obesity, IBD, diabetes, nutrition


Current Projects


Immunological & metabolic analysis of inflammatory bowel disease patients undergoing ileal resection
PIs: Scott Lee, William DePaolo
Funding: CMiST start-up funds

Functional analysis of commensals in patients undergoing colorectal cancer (CRC) screening & CRC biorepository
PIs: Cynthia Ko, William DePaolo
Funding: CMiST start-up funds


HIV-exposed microbiome impacts the severity of co-infections
PIs: Patricia Pavlinac, William DePaolo
Funding: R21, Eunice Kennedy Shriver National Institute of Child Health and Human Development (DePaolo & Pavlinac)

Inflammatory bowel disease (art and science, CMiST Vivo Art)
PIs: William DePaolo
Funding: The Kenneth Rainin Foundation

Immunopathophysiology of irritable bowel syndrome
PIs: Margaret Heitkemper, Jasmine Zia, William DePaolo
Funding: R01 (Heitkemper)