Center for Microbiome Sciences & Therapeutics, University of Washington
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Our comprehensive suite of services for microbiome research.

For microbiome research to move forward, we need to move beyond who is there to discovering what they are doing. We help you do this by teasing out and culturing the relevant bacteria for you to study.


Base Service

Bacterial Identification & Selection


Additional Services

  • Peptide Mass Profiling

  • Whole Genome Sequencing

  • Immuno-Phenotyping

  • Gnotobiotic Colonization

  • Microbiological Assays

  • 16s Profiling

  • Metabolic Analysis

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Base Service:

Bacterial Identification & Selection

  • Identify & generate bacterial isolate libraries

  • Refined bacterial culture techniques

  • Access to CMiST bio-repository of bacterial strains isolated from clinically relevant conditions

Each of us has a unique combination of bacteria that impact our risk of developing disease, our response to food, and the efficacy of drug treatments. Uncovering the functions of such bacteria and how they are personalized to us offers unrivaled therapeutic potential.

Microbial function discovery requires a culture-based approach that enables the isolation of clinically relevant strains that can be compared and interrogated to highlight their therapeutically actionable behavior.

Please email us for pricing,, and let us know if you are a member of CMiST.

What do I get?

  • Consultation to determine the optimal isolation strategy for your project and your bacteria of interest.

  • Principle isolation technique, usually a minimally selective technique that harvests a broad range of gut bacteria

  • Identification of 100 colonies per sample.

  • Catalogued agar plates with all identified bacteria (two per sample).

  • Expansion of up to 10 bacterial species per sample and creation of frozen stocks.

  • Storage of bacterial library, both catalogued agar plates and frozen stocks, for up to 6 months.

  • Full report and analysis of the cultivable bacteria identified in your samples.

  • Up to 10 bacterial isolates from each sample stored in optimal conditions for optimal recovery.

Additional Services:

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Peptide Mass Profiling

Peptide mass profiling of bacterial isolates to identify potential proteomic differences associated with specific strains or the clinical environment.

Includes: PCA, dendrogram, and spectra analysis.


  1. Client-selected isolates

  2. Entire experiment

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Microbiological Assays


  1. Bacterial Competition
    The ability of bacteria to compete and survive within a simple community or against a different species/strain will be determined based on in vitro growth assays.

  2. Bacterial Invasion/Adhesion
    The ability of bacteria to attach and/or invade cells (e.g. macrophages or epithelial cells) will be determined in vitro.


Whole Genome Sequencing

Sequencing of bacterial isolates for strain-level identification and to highlight key genetic features (e.g. presence of virulence and/or antibiotic resistance genes).


16s Profiling

16s rDNA profiling of the whole microbial community present in your sample.

Includes: simple bioinformatic analysis

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Co-culture of bacterial isolates and analysis of their soups for cytokine and soluble factors.


  1. THP-1 and epithelial cells

  2. Intestinal organoids


Metabolic Analysis

Bacteria will be grown in vitro and the ability to consume or produce particular metabolites will be analyzed based on mass spectroscopy.


Gnotobiotic Colonization

Functions of a bacteria can be assessed in vivo using gnotobiotic mouse models in collaboration with the University of Washington GNAC core.


How can these additional services help?


Peptide Mass Profiling
& Metabolic Analysis

BatchID uses cutting edge MALDI-TOF technology to resolve the peptide mass spectra of isolated bacterial colonies.  This provides rapid identification, as well as potential insight into the proteomic differences associated with strain pathogenicity, probiotic activity, or distinct environments.  BatchID peptide mass profiling compares the peptide mass spectra of bacterial isolates to highlight unique signals defining such behaviors. Furthermore our metabolomics partners can analyze metabolites produced or consumed by bacteria offering even greater insight into the mechanisms underlying microbial bioactivities.

Whole Genome & Next Generation
DNA Sequencing

Next generation DNA sequencing (NGS) offers revolutionary insight into microbial community composition and genetic capabilities. However, the number of different NGS options and the variables to consider can be overwhelming for the microbiome novice.  BatchID facilitates your NGS needs by advising on the optimal approach for your project and working with our industry partners to make it happen at a price you can afford.  We facilitate whole genome sequencing of bacterial isolates, shotgun metagenomic sequencing, and 16s rDNA amplicon sequencing.

In Vitro & In Vivo Phenotyping
(Bacterial Competition Assays,
Gnotobiotic Colonization)

Commensal bacteria alter human biology in many clinically significant ways.  BatchID can provide insight into how your bacterial target functions by profiling its in vitro and in vivo activity.  Our techniques include phenotyping bacterial-induced responses in immune cell, epithelial cell and organoid cultures, bacterial adhesion/invasion assays, and colonization studies in gnotobiotic mice. 

The Process

After completing a project form, we’ll meet and discuss the scope of your project and talk about pricing. Then, you’ll send us your biological samples and we’ll screen them using the appropriate growth conditions.  After your batch of samples has been identified, we’ll send you a list of the bacteria, their relative frequencies, and the isolates. From there, we can discuss possible next steps and additional services that may compliment your studies.


Step 1: Project Form

Please download and complete fillable PDF project form below and email it directly to:

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Step 2: Consult

After we receive your project form, we’ll email you to set up a time to talk over the phone or meet in person and discuss your project in detail.

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Step 3: Work Plan

Once we have an idea of how Batch ID can help move your study forward, we’ll design a work plan tailored to the needs of your project.


Step 4: Samples

Ship your samples to us and we’ll begin to build your strain-specific bacterial library.

We accept the following:

  • Fresh or frozen stool

  • Tissue (human & mouse)

  • Body fluid (human & mouse)

  • Fermented food samples (kombucha, kimchi, sauerkraut, etc.)

Instructions for shipping (PDF)



Step 5: Report

It will take up to 2 weeks to prep and run your samples. At the end of your project run, we’ll email you a report of your bacteria strains.

For projects greater than 5 samples, you will receive a preliminary report after 3 samples have been processed. At this time, we can refine the work plan if needed.

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Step 6: Isolates

We’ll ship back frozen stocks of your bacterial strains or you may choose to have us store your library for a reasonable fee.

Please note, if you shipped us raw samples, they will not be returned.


What types of samples can I send?

Fresh or frozen stool, tissue or body fluid (human or mouse) or food samples, which do not contain any category A infectious material.

What are category A organisms?

Category A organisms are those known to cause permanent disability, or life-threatening/fatal disease in otherwise healthy humans or animals. Organisms routinely present in human stool, tissue and body fluid are usually treated as Category B. 

How do I ship samples?

Samples should be shipped to CMiST Batch ID as category B biological substances.
Download shipping instructions (PDF).

How much sample should I send?

This depends on your sample type and can be advised during your initial consultation.  Our isolation methods are effective from as little as 20 mg of stool (about a teaspoon or the size of a grape).

What happens to any remaining sample after processing?

We cannot return you raw samples. If you require permanent stocks of your sample please aliquot them prior to shipping to the bacterial isolation core.

If you have other questions, please email us at