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Getting Your Microbes Analyzed Raises Big Privacy Issues

Say hello to your microbiome, Rob Stein. Our intrepid correspondent decided to get his gut bacteria analyzed. Now he's wondering if he needs to eat more garlic and onions.
Morgan Walker
Say hello to your microbiome, Rob Stein. Our intrepid correspondent decided to get his gut bacteria analyzed. Now he's wondering if he needs to eat more garlic and onions.

After spending months working on a series of stories about the trillions of friendly microbes that live in and on our bodies, I decided it might be interesting to explore my own microbiome.

So I pulled out my credit card and paid the $99 needed to sign up for the American Gut Project, one of a couple of "citizen science" or crowdsourced microbiome projects.

Organizers of the American Gut Project are recruiting thousands of people to donate their microbes to science — along with lots of personal information — to help researchers learn more about the trillions of microbes that inhabit the human body.

"The fact that they may play a big role in your susceptibility to disease and health is profound. I mean, it's astounding," says Jeff Leach, who helped dream up the American Gut Project. "It changes everything. I think it's a watershed moment for human health."

(To give us a glimpse of that hidden universe and its impact on health, we asked artist Ben Arthur to create an animated video of the human microbiome.)

A few weeks later, an envelope arrived in the mail with an instruction sheet and a long two-pronged cotton swab. After spending a week carefully logging the details of everything I ate and drank, I used the swab to collect a fecal sample and mailed it off for analysis.

While I was waiting for the results, I spent some time talking to bioethicists about some concerns I had heard about participating in these projects.

"I think sending pieces of your microbiome in to be analyzed and posted along with your health information is not for the faint of heart," said Hank Greely, a bioethicist at Stanford University.

For one thing, volunteers could end up finding out really scary-sounding things they never expected, he said.

"I don't know how likely it is, but we could say by looking at Rob Stein's microbiome that Rob is going to die of cancer in the next three years," said Greely. "That could upset Rob Stein, and his friends and his admirers, of whom there are many, no doubt."

Beyond that, Greely said, such projects also raise questions about privacy.

"If you have privacy concerns at all, you shouldn't do it," Greely said.

Here's why: Volunteers in these projects disclose lots of very personal stuff about their health, their daily habits and their families. It's all supposed to be kept strictly confidential, but there's no way to guarantee that these days, Greely said. Revealing any kind of personal health information could cause a variety of problems, including difficulties getting jobs, long-term care insurance or life insurance.

"Those are legitimate concerns," Greely said.

In addition, while the project is aimed at analyzing the genes of microbes, volunteers' DNA might end up in the sample and inadvertently become public, he said.

The fact that people are being encouraged to donate samples from everyone in their family, including children, worries Pilar Ossorio, a bioethicist at the University of Wisconsin, Madison.

Participants in the American Gut Project are asked to keep track of everything they eat for a week.
Morgan Walker / NPR
Participants in the American Gut Project are asked to keep track of everything they eat for a week.

"When it's a child, first of all, more will be learned as we go through that child's life about the implications of microbiome information," she says. "And there is a longer time during which that information may come back to bite the person."

And there's another angle that's really tricky, according to Eric Juengst, a bioethicist at the University of North Carolina, Chapel Hill. What if someone ends up profiting from research involving an individual's microbes? Should they get a cut?

"It may turn out that I actually have a potentially lucrative biome if I have the right bacteria. Maybe I should have some control over any profits that could be made from them," Juengst says.

Profits from, for example, a popular probiotic or yogurt made with the helpful bacteria.

So all of this was in the back of my mind months later, when I reconnected with Leach to hear what they had found about my microbes.

Leach asked me to open an attachment in an email. A series of multicolored bar charts popped up on the screen. Some showed my microbes while others displayed those of other volunteers, including Leach, for comparison.

It turned out my microbes are very different than Leach's. His are dominated by a totally different kind of bacteria than mine. And then something even more interesting jumped out at Leach.

"At the very top, in that little pink thing at the top of your bar, you'll see that a little over 4 percent of all the bacteria in your sample belong to the phylum proteobacteria," he said.

Proteobacteria includes "a lot of your bad guys," Leach said, such as E. coli and salmonella. They are associated with inflammation that may increase the risk of heart disease, cancer and other health problems.

Leach has no proteobacteria.

And at the bottom of my bar, Leach saw something else: I have very low levels of another species called actinobacteria.

"Those are typically considered good bacteria," Leach said. "So the more actinobacteria you have, the better." They're helpful, Leach said. "They're anti-inflammatory. They're known to suppress proteobacteria. So, those are often known as probiotics."

Actinobacteria are often added to yogurt, for example.

Leach has much more actinobacteria than I do.

So Leach started asking me about my diet. He eats the Paleo diet, which is heavy on stuff like meat and vegetables. People who eat a lot of onion, garlic and leeks tend to have higher levels of beneficial actinobacteria, he said.

"So I would suggest that you probably don't eat a lot of garlic, onions, and leek, at least not as much as I do. So would that be accurate?" Leach asked.

I love garlic and onions, and I do eat leeks occasionally. But Leach was right; I don't eat those foods nearly as often as Leach does. He eats them daily.

So by looking at my microbes, Leach was able to learn quite a bit about my diet, including the fact that I don't eat a lot of whole grains, and make some guesses about my possible health risks.

But Leach is the first to admit that this is all pretty speculative right now. No one can really say much of anything about anyone for sure just by looking at their microbes.

"Is this going to diagnose your disease? Absolutely not. Is this going to change your life? You know, maybe, maybe not. We don't suggest that this is something you can print out and run down to your doctor's office with," Leach said. "That's not what the project's about."

What the project's about, Leach stressed, is helping scientists learn more about our microbes — not only what they may be doing to us but also what we may be doing to them, such as disturbing them by taking too many antibiotics.

I asked Leach about all those ethical concerns. First of all, he said, the project is all about advancing science, not making money. And as far as the privacy concerns go, Leach said the project is taking pains to keep everything private.

"In place are the most stringent privacy protocols that you could possibly imagine. It's all under lock and key, if you will," he said.

But Leach acknowledged that there are never any guarantees.

"There's always a chance somebody might be able to figure out your sample, your results or whatever. So if those concerns are there, then we tell people, you know, not to join the study because it's not 100 percent foolproof — nothing is," he said.

So there you have it: I should think about eating more garlic, leeks, onions and maybe whole grains. And if I'm worried about all this getting out in public, I probably shouldn't have decided to put it on the radio in the first place.

Copyright 2021 NPR. To see more, visit https://www.npr.org.

Rob Stein is a correspondent and senior editor on NPR's science desk.