What is uBiome?

uBiome is the world’s leading microbial genomics company with a mission to advance the science of the microbiome and make useful products to improve human life.

What is uBiome’s Clinical Research Initiative?

The human microbiome consists of microorganisms living in the gut, skin, and in many areas of the body.. With the availability of rapid sequencing technology, it is now easier than ever to detect, quantify, and monitor patterns in the microbiota at multiple time periods. Now is  one of the most exciting times in microbiome research with over 1,100 registered clinical trials.

Since its inception in 2012, uBiome has partnered with hundreds of academic centers and over 1,000 researchers worldwide to conduct important microbiome research. Now, with the availability of clinical microbiome tests such as SmartGut and SmartJane, uBiome is making a call for research partners in the clinical space to expand clinical outcomes data in microbiome research and bring that knowledge to the bedside.

Our clinical research partners also use our Precision Sequencing™ technology, in our CLIA certified and CAP accredited laboratory.

uBiome aims to support selected microbiome-related clinical research ideas and proposals and provide in-kind research logistics and laboratory services. This is an ongoing initiative with rolling submissions and reviews. Entries are judged by our Medical Affairs, Research and Development, and Executive teams.

All eligible microbiome-related submissions will be accepted for review, but areas of emphasis include those using SmartGut (stool) and/or SmartJane (vaginal) kits as part of a study to impact costly and burdensome clinical areas for our healthcare system.

What is this Challenge about, and how does it tie to the uBiome clinical research ecosystem?

uBiome seeks to evolve available microbiome data such that microbiota can better guide clinicians through diagnosis and therapy—from wellness to illness to treatment and beyond—allowing clinicians to better focus on patient function, state, outcomes, and goals. We believe in the power of citizen science, as well as the scientific community, to help answer some of medicine’s biggest questions. This challenge creates a medical community to discuss some of these issues collaboratively. It allows clinicians to join teams, develop collaborations, and show the public that medicine is serious about microbiome research.

Genomics research may seem daunting to even the most seasoned clinician. The Microbiome Innovation Challenge, however,  encourages the medical community, regardless of research expertise, to submit ideas and research questions about the microbiome.

The Challenge seeks to:

  1. Inform the clinical and healthcare consumer community, as well as the healthcare innovation ecosystem about clinical applications of microbiome data.
  2. Understand the possibilities around the use of microbiome profiles for patient monitoring and risk stratification. This may include examining disease and health associations at certain time points and with certain phenotypes.
  3. Understand key microbiome responses to novel and standard therapeutics.

What is the problem this Challenge is trying to address?

This Challenge is an open clinical call for ideas and proposals that investigate a novel clinical use of microbiome testing. A number of burdensome chronic conditions across multiple organ systems (e.g. IBS, IBD, Parkinson’s, infertility, depression, rosacea, etc.) are linked to changes or an imbalance in the microbiome. With the availability of affordable at-home testing, the challenge brings together clinicians from all over the world to investigate clinical applications of microbiome science.

Entrants are asked to submit ideas that demonstrate how and when microbiome data are collected, what changes are expected, and (where possible) how this may become a therapeutic target in the future.

What kind of samples can I use in my research?

Although there are many human ecosystems of microbiota, this particular Challenge is focused on clinical use of gut microbiome (stool) samples using SmartGut and vaginal microbiome (vaginal swab) samples using SmartJane. If you wish to sample a different part of the body, please contact us.

What kind of sequencing does uBiome perform?

uBiome’s precision sequencing™ technology includes 16s and full shotgun metagenomic sequencing.

What data can I access?

You (and your patient) will receive the clinical reports on our portal. If you do not wish for your patient to receive clinical reports during your study, please notify us in advance at clinicalresearch@ubiome.com. You may also access the raw data in CSV, JSON and FASTQ formats. Please note in your submission whether you require assistance with data analysis.

What kind of ideas are entrants asked to submit?

Entrants are asked to present ideas on clinical applications of microbiome testing in one or more phases of a disease process or state of health. Examples of types of clinical applications:

  • Classifier: current state of microbiome of patients with disease X vs. patients without disease X. Can we predict disease with the given microbiome profile?
  • Risk stratification: do patients with complication X have a certain microbiome profile that predicts failure?
  • Intervention(s): does drug X or supplement Y alter the microbiome in such a way that correlates with symptoms?
  • Diet: does a dietary change improve microbial diversity that correlates with improved weight loss?

Who is eligible to participate?

Entry is open to clinicians and healthcare providers worldwide who are licensed and legally able to order laboratory tests in their state or country. Unlicensed trainees such as medical students and residents may submit if a licensed faculty sponsor is listed in the application.

Who is not eligible to participate?

The following are not eligible to enter the Challenge if, during the Challenge, they were or become:

  • Employees of the Challenge sponsor-administrator (uBiome)
  • Employees of companies or entities affiliated with uBiome or its contractors
  • Vendors of companies or entities affiliated with uBiome or its contractors
  • Direct family members (parent, son, daughter or sibling) of any such employees
  • Challenge Judges or their Direct Family Members
  • Anyone involved in designing, developing, judging, sponsoring or administering the Challenge (or their direct family members)
  • A citizen or resident of a country on the list of designated countries of State Sponsored Terrorism, as contained in the U.S. Department of State website
  • Any jurisdictions where the Challenge may be prohibited

How do I submit an entry?

To enter, complete all fields on the Official Entry Form on the website. Each entry should include any supporting material, including diagrams, videos, drawings, etc. Entry is only available online. Submissions in person, by mail, or other means will not be accepted. Each entry must be received during the Challenge entry period and must include the following:

  • Title
  • Contact information
  • Team name
  • Team leader
  • Names of all team members
  • Description of solution
  • Relevant external links (optional)
  • Image (optional)

The maximum size of uploaded files is as follows:

  • Maximum image file size: 40 MB
  • Maximum video file size: 300 MB
  • Maximum other file size: 200 MB

Are there entry fees? What expenses can entrants anticipate incurring?

There are no entry fees. If you are selected and choose to enter into a research collaboration with uBiome, you may incur costs related to participating in a research study at your location such as IRB fees or other standard costs. Depending on the complexity of the study, there may be other fees.

What are the prizes for the winners?

Winners will receive in-kind laboratory services, including sample kits and sequencing. Some winners may also receive additional services such as study design and analysis.

What is the timeline of the Challenge?


Planned completion date


September 15, 2018

Challenge Entry Period starts

September 15, 2018

Challenge Entry Period ends

September 15, 2019

During the Challenge entry period, submissions will be posted online for the public to vote on. Can I ask my friends and family to vote for my entry?

You are welcome to ask your friends and family to vote for your entry during crowdsource voting. An individual can vote once in crowdsource voting. Multiple votes by the same person, votes using fraudulent or false social media profiles, votes by bots or other automated means or any other fraudulent activity can be grounds for disqualification.

Will the crowdsource vote totals be posted?

Yes. The Challenge administrator will publicly post crowdsource voting totals for the public to see.

Will votes by the Challenge judges be posted?

No, votes by Challenge judges will not be posted.

Will the public be able to post a comment about my entry? What if I don’t like what is being stated about my Entry?

The public will be invited to vote and comment on each entry. Unless a comment is deemed by the Challenge administrator to be offensive or in poor taste, public comments will be posted.

After I submit my entry, how long will it be posted? Is there a guaranteed minimum amount of time my entry will be posted?

The administrator intends to post entries on a first-come, first-served basis. The Challenge administrator plans to post each Entry a minimum of two weeks on the Challenge website.

What will uBiome do with my submission?

The Challenge administrator (uBiome) will (1) post each qualified Entry on the Challenge website for crowdsource voting and comment and (2) submit the Entry for voting by the Challenge Judges.  

Who are the judges? What are their backgrounds?

The judges will be selected by uBiome and will include members of the Medical Affairs, Scientific Editorial, and Research & Development teams..

Can I talk to the judges in phase 1 of the Challenge?


Will I have to give up my intellectual property (IP) rights to enter the Challenge?

No. Entrants will continue to own the IP rights to their entries. uBiome only asks that Entrants give uBiome a worldwide, perpetual, non-revocable license to post the Qualified Entry on the Challenge website.

What happens if my rights to the IP rights to my entry are challenged?

At the Challenge administrator’s discretion, an Entry whose ownership is claimed by a third party may be (a) disqualified; (b) allowed to compete or (c) held in suspension while the Challenge administrator considers the matter.

What if I don’t want my entry to be published?

Each Entrant’s consent to posting of an entry is a condition of entry to the Challenge. If you don’t want your entry to be published on the Challenge website, you should withdraw your entry before it is posted.

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