I Sent a Sample of My Poop to uBiome

The Crux
By Sarah Scoles
Oct 7, 2015 4:59 PMMay 21, 2019 3:44 PM
(Credit: VGstockstudio/Shutterstock)


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My sample kit from uBiome stared at me from the kitchen table. Inside its sleek black cover, latched with Velcro, a single high-tech Q-tip awaited. On some morning of my choosing, I was to dab that Q-tip on a piece of used toilet paper, seal it up, and send tiny particles of my excrement back to the uBiome headquarters in downtown San Francisco. There, researchers would parse it and let me know what organisms squirmed around my intestines.

uBiome, a biotech startup, exists to help people explore their microbiomes — the population of tiny organisms that live inside you, outnumbering your own cells 10(ish) to 1(ish). I wanted to know how my own microbiome compared to other people like me: youngish people who run a lot who are generally healthy but sometimes eat large cheeseburgers.

But like other genetic test providers, including 23andMe and Ancestry.com, the company has a second and less visible objective. Users participate out of curiosity, health concerns — or, in the case of the still-nascent science of the microbiome, sheer novelty. But their data is the ultimate prize, which those companies, with participant permission, can study, share, and sell.

Background on the Biome

uBiome began in 2012, when founders Jessica Richman and Zachary Apte decided to take knowledge from the government’s Human Microbiome Project to the public, “enabling all of us to learn about our microbiomes and participate in science as soon as possible — without waiting years and years for the results to trickle down into products and services that people could use,” Richman told Female Founder Storiesin 2014.

Around that time, people had begun to understand just how big the microbiome’s effects are. Different gut demographics correlate with different mental and physical states, including depression and obesity. And the Human Microbiome Project had pioneered the tools need to analyze those demographics. “This is the first time in history that this kind of technology is available, and we want to make it accessible to everyone,” says the company’s Director of Research and Community, Alexandra Carmichael. “The more people participate and explore their microbiome, the faster research can go.”

The uBiome Experience

Today, from uBiome’s slick website, you can buy kits to find out what lives in your gut ($89); your gut plus two other “sites” of your choosing ($159); or all five “sites” — gut, genitals, mouth, nose, and skin ($399). Just rub the cotton swabs all over your most vulnerable parts, send your microbial details to San Francisco, and fill out a questionnaire that might make you feel bad about your lifestyle and habits; then, they’ll send you back information about your tiny hangers-on.

An open test kit from uBiome. (Credit: uBiome)

An open test kit from uBiome. (Credit: uBiome)

“Basically the samples come in to our lab, we break the cells open and extract the DNA, amplify the bacterial DNA using PCR (polymerase chain reaction), then run it through a sequencer to discover which kinds of bacteria are in each sample,” says Carmichael.

If you give them consent, they will also add your data to the “aggregate.” For you, that means seeing how your microbiome compares to others’. For them, that means using the data (in anonymized form) for large-scale studies and distributing it to third parties and research affiliates.

I consented and awaited my bacterial Yellow Pages.

The Results Are In

About a month later, I got an email from uBiome informing me that my sample analysis was ready. I logged in to my personal portal and took in my pie charts and tables.

Full disclosure, I didn’t pay $89 for my sample analysis kit. But if I had, I would have been disappointed. And if I had paid $399 for the five-site kit, I would have been even more so. The amount of readily available information provided little enlightenment about what my internal lurkers meant about me.

To be fair, this is not totally uBiome’s fault, and it’s something they disclose explicitly in the terms of service. We don’t know enough about the microbiome to say, “Too many of X and too little of Y mean Z,” or, “Firmicutes make you fat.” I knew that, and uBiome made very clear that no human should use their service to diagnose themselves or predict their future, and that knowledge of the microbiome is nascent and evolving. But I did expect the comparison tools to have more flexibility.

(Credit: Barmaleeva/Shutterstock)

(Credit: Barmaleeva/Shutterstock)

I could check out how my bacteria’s phyla stood up to those of vegans, paleos, vegetarians, heavy drinkers, weight losers, weight gainers, those on antibiotics, men, and women. But not women on antibiotics. Or vegetarian women who are in their 30s.

My microbiome doesn’t look like vegans’, paleos’, vegetarians’, lushes’, or any of the other groups’, which makes sense given that I’m an individual and don’t strictly fit within those categories. However, it also means that my data didn’t provide me much insight. I could download my own raw data and manipulate it, but then I was looking at it in a vacuum, without a set to compare to, so the analysis amounts mostly to, “Hey, look. I have this many of those bacteria. Neat?”

Beyond that, I could see a list of all my bacteria and what percentage of the population they were; which were “most enriched” compared to the aggregate; and which were “most depleted” compared to the aggregate. For some, I could click on their name — digging down from phylum to genus — and learn more about their lives and the effect they might have on mine.

However, many — more than half, if you go all the way to genus — don’t have entries. That’s because science hasn’t figured them out yet. And science will almost certainly figure them out in the future… By which time, however, my microbiome will probably have changed.

Bio Business Model

uBiome bills itself primarily as a citizen science project—your guts in your hands!

But there’s more behind their business model than your personal curiosity. Investments totaling more than $6 million from the likes of Andreesen Horowitz and YCombinator hint that the company’s ambitions are grander than just selling a bunch of swabbing kits.

For one thing, uBiome can carry out the dirty work of other researchers’ studies. Scientists can order kits in bulk and then uBiome does the extraction, sequencing, and analyzing of microbes. “Sometimes people come to us because they don’t have microbiome sequencing facilities in-house, or our process is faster or less expensive than doing it themselves,” Carmichael explains.

And uBiome’s kit-buying customers, like me, serve a valuable purpose in that enterprise, Researchers can compare their data to our aggregate, or just mine the aggregate itself. Carmichael says the company is “pretty flooded with research study requests.”

Finally uBiome, of course, has access to any signed-over data and can use it as they please, a fact that participants are well informed of and can opt out of if they wish.

But here’s the rub: While we know the microbiome is important (so important!), we’re just beginning our research into the specifics. And big data — your data — is the way to learn what a high firmicute to bacteriodete ratio means for health. Given that, it would be more appropriate for uBiome to pay you to swab your toilet paper than for you to give them $90 so you can learn what they can’t yet tell you.

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