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Researchers at UCSF Turn Directly to Consumers for Microbiome Project

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In an effort to organize a human microbiome project and to engage participants in the results, a small team of researchers affiliated with the University of California, San Francisco, has launched the uBiome project.

Billed as "the world's first effort to map the human microbiome with citizen science," the project has been raising funds from consumers and aims to initially sequence the microbiomes of 1,000 individuals, who will receive their results along with links to relevant health-related scientific studies.

UBiome is one of two recent efforts to harness individuals as both subjects and funders of microbiome studies. Last month, a consortium of researchers based at the University of Colorado at Boulder and elsewhere launched the American Gut project, which aims to characterize the microbiomes of US-based individuals and will also return results to participants (GWDN 11/2/2012).

Fundraising for both projects is currently ongoing at Indiegogo.com, an Internet-based funding platform. For a contribution of at least $69, potential uBiome participants will receive a stool sample kit, and for larger donations, they get additional kits to have their mouth, skin, nose, or genital microbiomes analyzed. The project accepts samples from around the world.

As of this week, uBiome had raised almost $50,000 from more than 300 individuals, about half the amount it aims to receive by Jan. 1, 2013, when its fundraising campaign will end.

By May of next year, participants will receive their sample kits and return them to the researchers, along with information about themselves and a signed consent form. The researchers will then use 16S rRNA sequencing to characterize the microbial diversity in the samples.

The analysis will be performed at the Quantitative Biosciences Institute at UCSF, where the project rents lab space and has access to equipment. The sequencing will be done on an Illumina HiSeq, either at UCSF or elsewhere, depending on the number of samples, according to Jessica Richman, an entrepreneur and one of the three co-founders of uBiome. Richman is currently pursuing a doctorate degree in mathematical sociology at the University of Oxford in the UK.

The other two co-founders are Zachary Apte, a biophysicist with a PhD from UCSF, and Will Ludington, an investigator at the University of California, Berkeley, who holds a PhD in cell biology from UCSF. The study also has a number of scientific advisors, including Joe DeRisi, a professor of biochemistry and biophysics at UCSF.

Over the summer, participants will receive their results, including the type and proportion of microbes in their sample; comparisons with health surveys of other participants with similar microbiome profiles; and comparisons with populations from scientific microbiome studies. Public data sharing will be possible as an opt-in but will not be required. Ludington also plans to use the data in his academic research at UC Berkeley, according to Richman.

The project will provide no medical advice or diagnoses, Richman said, just correlations with health-related microbiome studies, but its website states that obtaining a microbiome profile "might add useful additional data points" for someone with "a tricky health condition."

Richman said the project is considering partnering with other organizations in order to sign up specific participant groups, including the Crohn's and Colitis Foundation of America, as well as weight loss and obesity groups.

If the project takes off, it might also offer to track participants' microbiomes over time, which Richman said would "provide a lot of value."

The reason that uBiome turned directly to consumers for signing up volunteers and raising funding is that "it gives us an opportunity to do a lot of exploratory research that the public is interested in but the scientific establishment might not be," Richman explained.

While much of microbiome research today focuses on specific diseases, it might not necessarily answer an individual's questions about how his or her own microbiome changes with diet or other lifestyle changes, she said.In addition, crowd-funding is generally quicker than obtaining a grant from funding agencies such as the National Institutes of Health, although Richman acknowledged that traditional peer-reviewed funding comes with both credibility and institutional support.

A key difference between uBiome and the American Gut project, which has to date raised about $43,000 from participants out of a $400,000 goal, is that the latter focuses specifically on US residents, and that it also allows participants to submit samples from their dogs or other pets. For a donation of at least $99, prospective volunteers receive a kit that can be used for a stool, skin, or oral sample, which will be mailed out starting in January.

Like uBiome, American Gut will determine the microbial composition of the sample and correlate the results with participant-provided health information, which includes a detailed report on diet. It will also provide volunteers with their data, which will be deidentified before it is entered into a database, allowing users to log on and compare their data to that of others.

Data from American Gut, which currently has a much larger number of collaborating scientists than uBiome, will be open-source and will be included in the Earth Microbiome Project, an international study to characterize microbial life on earth systematically.

Richman claimed, however, that American Gut is more focused on conducting scientific research, while uBiome will be more "user-centric."

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