Tracing Your Microbiome Back to You

In a small enough study, scientists can trace the bacteria in your gut back to you. (Courtesy of Pacific Northwest National Laboratory)

By now most people have heard that their cells are outnumbered by the bacteria living in and around their body. Each of us is made up on average of 10 trillion human cells and the 100 trillion bacteria of our microbiome.

These bacteria aren’t just freeloaders and pests either. They are an important part of who we are and can play key roles in our health and well-being. In fact, many scientists refer to the genes and DNA of these bacteria as our “second genome.”

And if a study released last week in the Proceedings of the National Academy of Sciences (PNAS) turns out to be true, the DNA that live in the microbes in our body and on our skin may, like the DNA in our cells, actually serve as a unique identifier of who we are. This could raise a number of privacy concerns. But only if your microbiome is part of a smaller study.

It turns out that using the procedures in this study, you only really have a good shot at identifying someone out of a group of hundreds of people. Once the number of people in a study get beyond this, everyone becomes fairly anonymous again.

So people using do-it-yourself microbiome tests with companies like uBiome  that have tested tens of thousands of people, according to the company, are reasonably safe. The question right now is how protected is the privacy of people who have shared their bacteria in smaller studies.

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Stool Rules

The scientists in this study looked at the bacteria living in various places on the bodies of around 20-50 people at a time. They found that the gut microbiome (as measured in poo samples) was by far the best way to pick a person out of the group. The bacteria in the mouth was the second best with skin and vaginal samples being the poorest.

Bacteria from the skin were the hardest to trace back to the person they came from. (Wikimedia Commons)
Bacteria from the skin were the hardest to trace back to the person they came from. (Wikimedia Commons)

The bacteria living in the guts of the people they studied were varied enough to be able to tell people apart and stable enough that they could still tell them apart after nearly a year. In their studies, they could tell one person from another around 85% of the time using their poo. Not as good as looking at the DNA inside of a person’s cells but still remarkably identifiable.

An important feature of this sort of identification is that there are very few false positives. In other words, it is very rare to match a bacterial sample to the wrong person. Instead, you just tend to have it not match anyone over time.

Even the skin samples which were the least reliable could be used to identify a person one third of the time. Not stellar but again, still worrisome.

It is important to remember that these numbers are based on studying at most a few hundred people.  Once we get above that, the techniques used in this study won’t work. They can find a needle amongst 100 straws but not in a haystack.

All of this points to a general problem with DNA testing—it is hard to keep people’s identities secret. This now may even include the DNA from the bacteria in your poo.

DNA Data and You

Having your DNA tested is fun. You can learn about where your ancestors came from, a bit about your disease risks and maybe even whether you might have a red haired child one day.

DNA is a tricky thing to keep anonymous. This is even true of the DNA of the bacteria living in your gut. (Wikimedia Commons)
DNA is a tricky thing to keep anonymous. This is even true of the DNA of the bacteria living in your gut. (Wikimedia Commons)

Of course as is true with most things, there is a downside. Scientists can tell a lot about you from this DNA and as time goes on, they will be able to tell more and more. If the wrong people get a hold of it they might be able to learn about what you look like, your family history, who you’re related to, what diseases you might be susceptible to, and so on.

This is why people’s DNA data is anonymized before being included into publicly shared databases. Unfortunately as anyone who has ever had their credit card information stolen knows, no data is perfectly safe. In fact, anonymized data has been successfully hacked and specific DNA linked to specific people. (Click here for an example of DNA data hacking.)

Still, at least scientists are trying to protect genomic DNA. The same is less true for studies that involve the host of bacteria living in and on you, your microbiome.

Although not always successful, scientists do try to scrub any identifying contaminating genomic DNA from these studies and for a long time they thought this would be enough. But this new study suggests that it may not be. As we have seen above, scientists might be able to trace the DNA from your bacteria back to their original host, you.

While this probably isn’t as big a deal as getting a hold of your DNA sequence, it is still worrisome. Hackers can, for example, learn a lot about how and where you live from the specific set of bacteria you carry.  They may even be able learn about your risks for certain diseases.

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And as scientists learn more, they’ll probably be able to figure out more about us from our microbiomes. This might make connecting you to your microbiome more telling than you might think.

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