Center for Microbiome Sciences & Therapeutics, University of Washington


Identification & Selection
Host-microbe Interactions
Microbial Visualization
Study Design


Bacterial Identification & Selection

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Bacterial Identification + Selection

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.


Batch ID

With this service researchers can move beyond bacterial identification and towards discovery of bacterial function.

Learn more →


Vivo Art

Ideation and development of this pipeline came out of our ongoing collaboration with CMiST artist-in-residence, Kathy High. Through our art and science initiative, Vivo Art, we aim to not only communicate our research to the public but, also to advance science.

Learn more about Vivo Art →



Shel Lab
Bactron 900

300 square feet of dedicated biosafety level-2 space housing our Shel Lab Bactron anaerobic bacterial chamber, which can hold up to 900 plates.

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Bruker MALDI

Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry offers a safe, cost-effective, and adaptable system for rapid identification of bacteria and fungi. Recent studies have shown that MALDI TOF may outperform conventional identification assays.

Host-Microbe Interactions


Understanding the complex tug-of-war between the host and microbes is critical in our ability to develop effective therapies to treat or cure disease.


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.

Equipment & Technologies

  • Human intestinal organoids for drug and bacterial screening

  • LICOR Odyssey Fc Imaging system

  • Gnotobiotic facility, affiliated resource through
    UW Gnotobiotic Animal Core (GNAC)

  • Luminex multiplex cytokine assays


Intestinal Organoids
aka ‘Mini Guts’

STEMCELL Technologies

STEMCELL Technologies


Microbial Visualization

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Microbial Visualization

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.


Leica Laser Microdissection Microscope (LMD7)

The Leica Laser Microdissection Microscope is a contact- and contamination-free method for isolating specific single cells or entire areas of tissue from a wide variety of tissue samples. The samples can then be available for further molecular biological methods such as PCR, real-time PCR, proteomics and genomics.


Leica Fluorescence Microscope (DM4)

Generate or acquire fluorescent probes against specific bacterial members of the microbiota in order to visualize their relationship with each other as well as with the intestinal tissue using fluorescent microscopy.


Leica Laser Microdissection Microscope

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.


Study Design


Study Design

Experimental Consultation & Bioinformatics

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)


Approach to Research

Interested in our services, but also in collaborating or partnering with us? Learn more about our current collaborations.