Center for Microbiome Sciences & Therapeutics, University of Washington


Our Approach
Project Highlights
Collaborator Q&A


Our Approach


Project Highlights


IBD & Microbiome

Scott Lee, UW GI
William DePaolo, UW CMiST


Study 1

Interrogating the microbiome & immunity in recurrence of ileal disease post resection


This study aims to further evaluate and define immunological, metabolic or inflammatory signatures that predispose patients with Crohn’s disease to post-surgical dis-ease recurrence as compared to those patients who do not have significant post-surgical recurrence.

Our goal is to create a hypothesis of how metabolomics influence and can predict recurrence of Crohn’s post-surgically. This will lead to more focused and refined studies to better define this question.


Study 2

Correlations between changes in the microbiome of IBD patients & biomarkers of disease


This study aims to investigate the methodology behind the biomarker assays (e.g., calprotectin, c-reactive protein, anticommensal antibodies) and study specific metabolites and bacterial composition sf patient fecal samples.

  • Examining the relationship between biomarker levels and the microbiome in patients with IBD

  • How current biologics alter the microbiome


Dr. Scott Lee is an associate professor of medicine with expertise in inflammatory bowel disease (Crohn’s disease and ulcerative colitis). His research is focused on inflammatory bowel diseases (IBD) including new therapies for IBD, improving outcomes in the treatment and long term management of IBD, evaluation of non-invasive biomarkers to assess disease activity in IBD patients and the effects of the microbiome on IBD.

We understand 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.


This project is partially funded by


HIV & Microbiome


HIV-exposed microbiome impacts
the severity of co-infection

Patricia Pavlinac, PhD, MS
UW Global Health

William DePaolo, PhD

Do changes in the microbiome caused by infection or antibiotic use after the expression of genes in the enteric pathogen lead to an increase in virulence?

This project seeks to address an important gap in our understanding of enteric infections that occur in an intestinal environment with a low bacterial diversity. It proposes a conceptually innovative hypothesis that the chronic viral infection itself does not drive Enteropathogenic Escherichia coli (EPEC) virulence, but rather the reduced gut microbial diversity caused by the infection. Importantly, this project will evaluate whether restoration of diversity via fecal microbiota transplants can be used a treatment strategy.

To answer these questions an integrated, interdisciplinary approach in mice, humans and bacteria using genomics, microbiology, and immunology will be used. If successful, these findings may redefine how we evaluate and treat at enteric disease not just in HIV but any disease associated with a reduced microbial diversity, and may provide a biological framework to develop microbiota-based therapies.


Patricia Pavlinac, PhD MS, is an epidemiologist and co-director of the Healthy Growth & Development Core of the Global Center for Integrated Health of Women, Adolescents, & Children (Global WACh). Dr. Pavlinac’s research aims to identify interventions to halt morbidity and mortality attributed to enteric and diarrheal diseases. Her other research interests include pediatric tuberculosis, particularly the diagnosis of tuberculosis in pediatric populations.

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Collaborator Q&A


L. Roth, MD

Dr. Christian Roth is a pediatric endocrinologist at Seattle Children’s Hospital. His research is focused on childhood obesity, diabetes and puberty. It includes metabolic factors in body weight regulation and hypothalamic control of feeding circuits, genes involved in childhood obesity and diabetes, and post-craniopharyngioma obesity.

Christian L. Roth, MD

Christian L. Roth, MD

Q: How did you become interested in science?

I was always interested in understanding normal physiology and mechanisms of disease, and in developing effective treatments against disease in humans. As there is still a lot unknown this automatically leads you to do research.

What was the primary challenge with this project?

Finding a probiotic that is standardized in bacterial content and getting this drug provided
for our study.


Q: What is the project that you are currently working on with CMiST?

We are currently investigating the role of gut microbiota in adolescents with obesity and risk for developing diabetes mellitus. We test if treatment with a probiotic can change risk factors of metabolic syndrome and risk for developing diabetes and diabetes-related problems.

Q: What has it been like to work with CMiST on this project?

CMiST provides the necessary state-of-the-art technologies and expertise for performing the microbiota analyses in fecal samples and for identifying the metabolic signatures of the bacteria.

One of our fellows has the chance to work with the CMiST team. Thereby there is a great cross pollination regarding development of different research ideas, using cutting edge technologies, including bioinformatics, proteomics, and novel in vitro and in vivo test models.

Q: What do you see as the next “big thing” in microbiome research? 

Understanding the complexity of how the microbial products, metabolites produced by bacteria that live in the human body, interact with the host and thereby may cause or prevent disease.

If you’re interested in collaborating with us, please send us a note with a brief description of your project.