Microbiome analysis: How one tech company is changing health behaviors, one fecal sample at a time

This new technology lets citizen scientists experiment with their own gut bacteria or be part of larger efforts to figure out how the microbiome affects various health conditions.

In three years, scientists at the San Francisco-based company uBiome have analyzed the microbiomes of over 50,000 participants in 65 countries. For $89, anyone can send in a fecal sample, gathered by swabbing a used piece of toilet paper, and get a report about the unique makeup of their gut. It's like the bacterial version of a fingerprint.

More recently, scientists at uBiome have developed the ability to tell their customers how their particular bacteria makeup performs. In other words, how they metabolize nutrients--carbs, fats, proteins and vitamins-- compared with other groups of people who've been analyzed. Most of the company's customers are people who are just curious about what's in their gut and how their actions--things like diet, probiotic consumption or smoking--might influence its contents.

Image: uBiome

"What we normally tell our users is that the best thing to do with this sort of data is to do a controlled experiment," said uBiome's senior bioinformatician Daniel Almonacid. "So for instance they remove some food from their diet or they increase the amount of one particular food in their diet and they see what changes." The company sells "gut time lapse" kits, where buyers can take fecal samples from before, during and after their experiment and have them analyzed.

It's the latest example of how the power of data is transforming the ability of people to have greater visibility into their own health care and take control of certain aspects of it.

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The company has also started doing exploratory studies on a bigger level. Recently, they recruited women for a study of the relationship between vaginal bacteria and menstrual cycles. Almonacid says 540 women signed up in three hours.

"I think there's this huge, latent fascination with science that most people don't get to exercise," said CEO Jessica Richman.

Currently, participants are being recruited for studies of the microbiomes of people with conditions like irritable bowel syndrome, eating disorders and clostridium difficile colitis. Richman says her favorite so far is the "eye crusties study." The objective of that one is just to find out what bacteria is in that gunk that forms in the corner of our eyes.

"The real benefit of this citizen science platform as we grow is whether the question is kind of silly--like studying eye crusties--or whether the question is extremely serious, you can sort of do them all on this platform and get results that are of interest to individuals or to the whole health system," she said.

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A note about security and privacy: Richman said that like all traditional medical research, the company's studies follow a protocol set by an institutional review board, which ensures protection of participants' personal information.

Richman and Almonacid see a future for microbiome analysis in doctors offices and hospitals as well as the homes of curious citizens.

"We've had the good problem, I guess, of a lot of doctors wanting access to our technology to use it for their patients," said Richman.

Currently, the company only offers its product to consumers as an exploratory tool. But rather than becoming just a diagnostic tool, Richman sees microbiome analysis as part of the movement, along with all the other health tracking devices that have come along recently, to help patients better manage their own health.

"There's a trend that is described by many names," she said. "Citizen science, patient empowerment, the e-patient, patient-centric medicine, precision medicine, and they all boil down to something very similar which is the patient is much more in control of the process of healthcare."

Almonacid has one really bold prediction for the future of the technology: "Two or three years from now, everybody's going to be (genomically) sequenced as soon as they're born and the microbiome will be sequenced at several points during (their) lifespan."

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