UW Research

Center for Microbiome Sciences & Therapeutics (CMiST)



CMiST will serve as a hub of collaboration and connectivity for researchers and clinicians at the University of Washington and its affiliated campuses.

Core Services Offered

Bacterial Isolation & Cultivation
We have established a unique set of tools and reagents that can be used by clinicians, researchers, and industry to address the complex relationship between intestinal microbiota and host tissues in diseases such as Inflammatory Bowel Disease (IBD), diabetes, gastric and colon cancer, celiac disease, HIV/AIDS, infectious diseases such as Shigella, Enteropathogenic Escherichia coli (EPEC) and Enterohemorrhagic Escherichia coli (EHEC), malnutrition and vaccination.

The ability to link microbiome isolates from a patient to their own clinical data and existing tissue pathology is a new level of personalized medicine. This will enable investigators to study the disease phenotype, tissue status and bacterial response from the same patient, over time and track changes due to disease state, as well as response to therapy and treatment.

With this service, which we are calling Batch ID, researchers can move beyond bacterial identification and towards discovery of bacterial function.

Host-Microbe Interactions
With this service, we will explore the immunological and genetic consequences of the microbiome when in contact with human cells. Normally, we co-exist with the 100 trillion bacteria that call our bodies home. However, genetics and/or extrinsic factors (e.g. infection, diet) can influence this relationship and cause changes leading to the development or exacerbation of inflammatory intestinal diseases.

Microbial Visualization (microscopy)
Ecology and community are essential and important aspects to the microbiome and cannot be truly understood using computational models and synthetic biology. Therefore imaging the microbiome will be a critical tool to get us past the descriptive and theoretical science that is so common today.

Fluorescence and transmission microscopy are noninvasive methods ideally suited to resolve the dynamical processes in microbial communities that will allows us to observe spatially structured communities using rRNA fluorescent in situ hybridization (FISH) as well as fluorescent or fluorogenic probes for visualizing small molecules.

Using our Leica Laser Microdissection Microscope (LMD7), you can isolate specific cells, mucus layers, inflammatory foci or cancers from histology slides. You can use your already established tissue banks to generate new data, or through our services you can access to UW Medicine biorepositories.

Study Design
Advice and information on starting a microbiome project or on how to use our technological resources and those of our affiliated centers and research groups to develop projects that test biological function:

  • Review sequencing data and discuss microbes of interest
  • Bioinformatic analysis of your data sets (coming soon)

Learn more about research approach.

CMiST Services

Funding Information (Sources of Funding)

  • Private gift
  • UW Department of Medicine
  • UW Provost
  • NIH NICHHD 2018-2020
  • Institute for Translational Health Sciences 2018-2019
  • Cure 4 IBD

Reporting Structure

Chair of Medicine

Related UW Entities

Schools & Colleges

UW College of Engineering
UW School of Art + Art History + Design
UW School of Medicine
UW School of Nursing
UW School of Public Health


Arts (Resselaer Polytechnic Institute, Troy, NY)
Behavioral Nursing
Comparative History of Ideas
Comparative Medicine
Environmental Health & Occupational Health Sciences
Global Health
Human Centered Design & Engineering
Medicine, Allergy and Infectious Disease
Medicine, Gastroenterology
Medicine, Metabolism, Endocrinology & Nutrition
Medicine, Pediatrics

External Partners

Fred Hutchinson Cancer Center
Institute for Systems Biology, Seattle, WA
Rensselaer Polytechnic Institute, Troy, NY