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10:16 pm
Sun November 3, 2013

Getting Your Microbes Analyzed Raises Big Privacy Issues

Originally published on Tue November 5, 2013 10:28 am

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.

"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 2014 NPR. To see more, visit http://www.npr.org/.

Transcript

DAVID GREENE, HOST:

On this Monday, it's MORNING EDITION from NPR News. Good morning. I'm David Greene.

STEVE INSKEEP, HOST:

And I'm Steve Inskeep.

Today in Your Health: Getting your microbiome analyzed. We've been hearing a lot lately about how the microbes that inhabit our bodies may influence our health and well-being, sometimes for the better.

NPR's Rob Stein has been exploring this hot new field of biomedical research, and it got him wondering about his own microbes. So he decided to take a look.

ROB STEIN, BYLINE: Anyone who wants to get their microbes analyzed can sign up for something called the American Gut Project. That's how I met Jeff Leach.

JEFF LEACH: You should join the study as well, and take that journey.

STEIN: A journey through the trillions of microorganisms living in my body, what scientists call my microbiome. It was an intriguing offer.

LEACH: You end up with, you know, a snapshot of all the various bacteria in your gut.

STEIN: A snapshot that could give me important clues about how my microbes may be influencing my health.

LEACH: The fact that they may play a big role in your susceptibility to disease is profound. I mean, it changes everything. And so I think it's a watershed moment for human health.

STEIN: Leach helped dream up the American Gut Project, one of a couple of projects recruiting thousands of people to donate their microbes to science, along with lots of personal information. So researchers can really dig into what our microbiomes are up to.

So I pulled out my credit card, paid the $99, and signed myself up. A few weeks later, a small manila envelope arrived in the mail.

(SOUNDBITE OF RUSTLING PAPER)

STEIN: OK, let's see what I got here. There's a three-page instruction sheet, a password and an ID number to get my results. Looks like the first thing I have to do is keep a diary of every little thing I eat and drink for a week.

OK, what's this? A big plastic tube. I pop it open and pull out a really big, long, two-pronged Q-tip. So, the next thing I have to do is take that big double Q-tip to the bathroom to, um, collect a sample. Well, no need to go into any more detail about that. So, I do all that and send off my sample.

While I'm waiting, I start asking around about the pros and cons of signing up for one of these projects.

HANK GREELY: I think sending pieces of your microbiome in to be analyzed and posted along with you health information is not for the faint of heart.

STEIN: Hank Greely's a bioethicist at Stanford. He says there are a bunch of concerns about this sort of thing. One is that volunteers could end up finding out really scary-sounding things they never expected.

GREELY: 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. That could upset Rob Stein and his friends and his admirers, of whom there are many, no doubt.

STEIN: Well, maybe, maybe not. But Greely says anyone considering signing up should definitely stop and think first. Before we get into all that, let's hear about what my microbes showed.

Hi, Jeff. You there?

LEACH: Yeah. Hey, Rob. I'm here.

STEIN: When my results come in, I connect back up with Leach via Skype. He's in Tanzania, studying the microbes of tribes living in the bush. Leach asks me to open an attachment in an email. A bunch of multicolored bar charts pop up. Some show my microbes, others Leach's, for comparison.

LEACH: Are you able to run your mouse across any of those bars and have a little pop-up window that shows percentages?

STEIN: Yeah. When I roll my mouse over the bar graphs, little things pop that have, looks like names of species of bacteria and percentages.

LEACH: Right.

STEIN: Turns out, my microbes are way different than Leach's. His are dominated by a totally different kind of bacteria than mine. And then something even more interesting jumps out at Leach.

LEACH: And 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.

STEIN: Proteobacteria. What's that?

LEACH: Proteobacteria is a group of bacteria that includes a lot of your bad guys, like E. coli and salmonella and so on and so forth, the ones that are associated with inflammation.

STEIN: And inflammation is associated with an increased risk for all sorts of diseases, including heart disease and cancer. So it's probably not good news for me that I have so much proteobacteria. And Leach, he has none - zero, zip. And at the bottom of my bar, Leach sees something else.

LEACH: You have very low levels of actinobacteria.

STEIN: Actinobacteria?

LEACH: Those are typically considered good bacteria. So the more actinobacteria you have, the better. These are healthful. They're anti-inflammatory. They basically wage war, if you will, for the lack of a better term, on proteobacteria. So, those are often known as probiotics.

STEIN: You see them a lot in yogurts. Leach has way more actinobacteria than I do.

So compared to Leach, I don't look that great. He's got way more of the good bacteria and none of the bad ones that I have. Meaning he may be less prone to some diseases than I am.

So Leach starts asking me about my diet. He eats the Paleo Diet, which is heavy on stuff like meat and vegetables.

LEACH: So people who typically eat a lot of onion, garlic and leek will have higher levels of beneficial actinobacteria. And so you see that in mine. 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?

STEIN: Well, I love garlic and onions, and I do eat leeks occasionally. How often do you eat those things?

LEACH: Yeah, I eat onions every day. There isn't a day that doesn't go by that I don't eat onions.

STEIN: OK, score one for Leach's diet over mine. He keeps going.

LEACH: Do you eat a lot of whole grains or do you not? And I would say looking at this, I would guess you're not a big whole grain eater.

STEIN: Well, I do eat a lot of whole wheat bread, but not much in the way of heavy-duty whole grain cereals and that sort of thing. So Leach was able to learn quite a bit about my diet and my possible health risks by looking at my microbes. But Leach is the first to admit, this is all pretty speculative. No one can really say much of anything about anyone for sure just by looking at their microbes.

LEACH: Is this going to diagnose your disease? Absolutely not. We don't suggest that this is something you can print out and run down to your doctor's office with. That's not what the project's about.

STEIN: What the project's about is helping scientists learn more about our microbes. Not only what they may be doing to us, but what we may be doing to them - such as messing them up by taking too many antibiotics.

All this gets me thinking about those concerns that Hank Greely, that bioethicist at Stanford, mentioned. So I ask him to tell me more.

GREELY: If you have privacy concerns at all, you shouldn't do it.

STEIN: Here's why. Volunteers disclose lots of very personal stuff about their health, their daily habits, their families. It's all supposed to be kept strictly confidential. But Greely says there's just no way to guarantee that these days. And revealing any kind of personal health information can cause big problems.

GREELY: Job discrimination. Long-term care insurance discrimination. Those are legitimate concerns.

STEIN: And there are even more concerns. The project is analyzing the genes of the microbes. But bits of your DNA might end up in the sample and be made public.

And there's a whole other angle that's really tricky. Eric Juengst is a bioethicist at the University of North Carolina in Chapel Hill. He wonders: What if someone ends up profiting from research involving our microbes? Should we get a cut?

ERIC JUENGST: 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.

STEIN: Profits from, say, a popular probiotic, or yogurt made with the helpful bacteria. So I ask Leach about all this. First of all, he says, the project is all about advancing science, not making money. And the project is taking pains to keep everything private.

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

STEIN: But Leach acknowledges that there are never any guarantees.

LEACH: 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.

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

Rob Stein, NPR News.

(SOUNDBITE OF MUSIC)

INSKEEP: And for an animated tour of the human microbe, go to npr.org. You're listening to MORNING EDITION from NPR News. Transcript provided by NPR, Copyright NPR.

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