Fingertips Leave A Bacterial Fingerprint

Researchers studying the microbes that inhabit human skin say the bacteria left behind when an object is touched can be used to identify who did the touching. Microbe researcher Rob Knight explains how these bacterial "fingerprints" could one day be used in solving crimes.

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IRA FLATOW, host:

You're listening to SCIENCE FRIDAY from NPR. I'm Ira Flatow.

Up next, something I'm sure you're going to see this ripped from the headlines, as they say on television, soon on CSI, it's going to be coming soon, I'm sure. It's the bacteria fingerprinting or bacteria signatures. You know that bacteria - you know, they live all over your body, they're on your hands and even if you wash them regularly, you can't really get rid of them. And these bacteria can be transferred to anything you touch.

Now the researchers have shown that by looking at the bacteria on an object -let's say, a keyboard on your computer - they can figure out who touched that object. The bacteria on your hands are unique to you, and that bacterial signature you leave behind can be traced back to you.

Joining me now to talk more about it is Rob Knight, he is Early Career Scientist at the Howard Hughes Medical Institute, and associate professor of chemistry and biochemistry and computer science at the University of Colorado in Boulder. Thanks for talking with us, Dr. Knight.

Dr. ROB KNIGHT (Early Career Scientist, Howard Hughes Medical Institute): Hi, Ira. Thanks for calling.

FLATOW: I guess most of us don't realized, you know, all that bacteria that's on our skin.

Dr. KNIGHT: Well, it's amazing. (Unintelligible) inside what we like to think of as our bodies, there's actually about 10 times as many bacterial cells within our human cells. So, you know, there's about 10 trillion of our cells, and then there's about 100 trillion bacterial cells, mostly in the gut. But as we showed in this study, most bacteria's on the skin - are also really unique and really interesting.

FLATOW: So who gave you an idea to look at objects and see if we leave bacteria behind when we touch them?

Dr. KNIGHT: Well, that's a great question. This actually started off as a biogeography project. So, my colleague, Noah Fierer, in ecology and evolutionary biology thought that the keyboard would be a great model for looking at the kinds of patterns we see between different islands and different continents, and so forth. And so if look at the keyboard, you just start to think about say if you look at the keyboard you just start to think about things like, the G key or the H key, right they're right next to each other on the keyboard, but you touch them with opposite hands.

So what's more important the spatial location, or what you touched them with. So then it went on from there, so looking at the fingertips of the people who touched the keyboard that they control. And then from there, it was amazing. What we thought was going to happen was maybe there would be some association between the fingertips and the keys but we thought that, you know, the fingertips, you've got all these crevasses and things, right? So that's a really nice environment for bacteria...

FLATOW: Right.

Dr. KNIGHT: ...where as the keys, there they completely smooth them almost like a desert. So what we thought of the fingertips on the keys would be totally different, but maybe with some traces left behind. Instead what we saw is that all the fingertips and all the keys from the same person clustered together beautifully, and that was really one way to sort of think that maybe, hey, we can use this for identification. And this could be potentially important for a practical application as well as there...

FLATOW: Mm-hmm.

Dr. KNIGHT: ...general ecological principles.

FLATOW: And you were able to match the bacteria on the keyboard to a specific person?

Dr. KNIGHT: That's exactly right. So what we saw is that bacteria from individuals keys and this was really amazing, right, that you can take a Q-tip and take the bacteria from one individual key, extract the DNA and use that DNA to figure out what bacteria are there. It's amazing that even from a single key, or from a single fingertip you can get enough DNA to match the fingertip, the keys from a same person together. And then considering what those kind of computer thing, we moved on to looking at computer mice, right?

FLATOW: Right.

Dr. KNIGHT: Now, the question there was, if we if we matched up the mouse with the hand? And for that we used a database of undergraduate's hands we'd sampled a couple of years ago in another study. And what we found was that, yes, indeed, you can very effectively match up the mouse to the hand that touches that mouse.

FLATOW: Wow. Is it as good as a fingerprint, though?

Dr. KNIGHT: Well, you know, that's a fascinating question, because when we were writing up the study, it as remarkably hard to get quantitative data about how good fingerprints actually are.

FLATOW: Right.

Dr. KNIGHT: They - a lot of fingerprints analysis is not automated, it's based on expert's opinion. And coincidentally, it was actually a paper and I'm sorry, a news commentary in (unintelligible) this week talking about how a fingerprinting itself, may be less precise than we generally think and by it needs to be reevaluated this month (unintelligible). So it's difficult to do like comparison, primarily because the information just as the (unintelligible) positional thing your prints.

FLATOW: Right. Rob, how many touches does it takes? If you touch the mouse or the key once, is that enough of a bacteria transfer to make an identification?

Dr. KNIGHT: Again, that's a really good question. At that stage were in very early stages of development of those kinds of procedures that we decided to start what the objects we thought would be easiest to identify" The ones that one person touches that object every day. So we haven't yet tried to that.

We haven't yet, in general, tried it out for cases where you just touch the keyboard once, or just or just touch your mouse once. We did tried glass pieces. It's having a hand having a subject handle like a glass beaker, the way you would in a drinking glass, one single time, wasn't enough to get usable DNA from. So somewhere between touching something once and touching something every day, there's going to be that point where you can pick it up. So we need to do a lot more technology development to do that.

FLATOW: Let's go to the phones. Jason(ph) in Dallas. Hi, Jason.

JASON (Caller): Hi. Good afternoon, gentlemen. I'm a homicide detective. And when I first heard about this, a question arose in my mind because I don't know if I have correct information or not. But unlike fingerprints that can not be replicated, it's my understanding that bacteria can be replicated. Is that correct?

Dr. KNIGHT: Yes, that's correct, in the sense that you can start off with a very small amount of DNA and then amplify that DNA and get a lot more of it. One of the other things that's interesting is that the bacteria on the same person see to be relatively stable at the time. And, also, when you look at identical twins, even though they are the same on their human genome, at least in the gut(ph) communities, their gut communities can be of much as 70 percent different. So in that way, your microbial communities and your microbial DNA are even more identifying than your human DNA.

FLATOW: Can I transfer it, make a phony bacteria print to something else?

Dr. KNIGHT: Well, that's a good question. We actually looked at that in our science paper last year, trying to transfer bacteria from one person to another. And what we found is that when you transfer mouth bacteria to the, sort of, forehead, the forehead bacteria, will outgrow it as mouth bacteria in about two hours, whereas they stay on your forearm for about eight hours.

We weren't able to effectively transplant the whole bacterial community from one person to another in that study. So, in other words, if you transfer it from someone else's forearm to your forearm, what happens is that might actually help your own forearm bacteria grow back faster. So we couldn't find any evidence that you could fake a bacterial fingerprint in that sense, by getting it - by, say, shaking someone's hand really vigorously and then committing a crime.

However, the technology to do any of this has only existing so recently. Most of this relies on techniques that we and other people developed over the last couple of years. So just about anything you could imagine would be a really great experiment that hasn't been done yet and would be really exciting.

FLATOW: Jason, you homicide detectives have some more homework to do, I guess.

JASON: Yeah, looks like it's going to keep us busy. You know, one of the other things that (unintelligible) question, if the bacteria lands on, like, a keyboard, that is already contaminated with some other kind of biological material, does the bacteria mutate or change?

Dr. KNIGHT: Well, bacteria are mutating and changing all the time. I think - so again, we were really surprised to see (unintelligible) bacteria match the fingers - match the fingertip bacteria so well. Because we had expected that only a very small number of bacteria would be able to survive on the keyboard long term.

So although that's a very reasonable idea, it's not actually what (unintelligible) evidence for in our study. And finding out in general how persistant the traces are going to be really important. So, for example, we shaved the skin samples that were just sitting around in the lab for two weeks, and also the fecal samples that have been sitting around in the lab for two weeks. We can still tell which particular person they had come from even two weeks later without any refrigeration or anything. So, you know, if you've been finding that kind of material on your desk, even if it's couple of weeks later, we can probably tell who the material came from.

FLATOW: Hmm. What about people who cohabitate, live together a lot, do they have - do they start growing the same bacteria on their skins?

Dr. KNIGHT: Well that's a good question. Again, that hasn't been looked at with modern high resolution molecular methods to my knowledge. It's very plausible that you would converge on the same community. But the preliminary result that we have doesn't really support that idea. We're doing a lot of that actually of that kind of thing with the Crohn's and Colitis foundation. They've been amazingly generous in supporting time series studies where - where for diseases like you see in Crohn's disease. The dynamics from the communities in the gut are likely be really important. And so trying to figure out the kinds of things like, can you get recolonized by the people that you live with?

FLATOW: Right.

Dr. KNIGHT: And can you predict what's going to happen from a sample that you take at one particular time? Can you predict the future from that sample? That's something that we're extremely interested in finding out.

FLATOW: It looks like you've opened up a whole new area of untouched research potential.

Dr. KNIGHT: Well, that's what's so exciting about it especially part of the Colorado initiative molecular biotechnology, and what we're really trying to do is encourage students to take really interdisciplinary approaches. And what's so nice about this kind of research is it really combines microbiology, ecology, computer science, all these different fields that they can pick up techniques from and apply them to all these great questions that anyone can come up with. But that in general, we don't know the answers to it yet.

FLATOW: Yeah. Well, based on your preliminary research, it's not ready for primetime juries, yet. It's not ready for courtroom presentation.

Dr. KNIGHT: Absolutely. I don't think we could convince a jury of it today. But, you know, maybe five or 10 years down the track, especially considering how much cheaper DNA sequencing is getting, I think we'd be able to get the sample sizes to where we could really move it up to a large scale.

FLATOW: Could you get bacteria off of other things on our body in using just -not just your fingerprints?

Dr. KNIGHT: Oh yeah, absolutely. So one thing that's fascinating that we found in that paper last year actually was the bacteria in different parts of your body are much, much more different than we expected. So you're forehead has totally different community again from what on your - what's on the palm of your hand or your fingertip.

And then, once in your mouth or what's in your gut are different again. So one thing that Cathy Lozupone, who's the really talented post (unintelligible) in my lab, who completed her PhD on this a couple of years ago, found out is just how different those different types of bacteria are compared to what's out there in the environment. So, we literally carry all these totally different (unintelligible) within us. The difference between what's on your hands, what's in your mouth, is like the difference between, say, what's on a polar ice cap. This is what lives in a hot spring in Yellowstone - totally different communities

FLATOW: Fascinating. Good luck to you. Thank you for coming on and talking with us.

Dr. KNIGHT: Great. Thanks so much for your interest, Ira.

FLATOW: Rob Knight is an early career scientist at the Howard Hughes Medical Institute. He's also an associate professor of chemistry and biochemistry and computer science at the University of Colorado at Boulder. And he was talking to us about the new fingerprint technology using - well, we shouldn't be using fingerprints - bacteria.

I'm Ira Flatow. This is SCIENCE FRIDAY from NPR.

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Bacteria On Your Fingertips Could Identify You

Hands on a keyboard i i

hide captionResearchers were able to correctly match bacterial DNA on keyboards and computer mice with their individual users. This bacterial "fingerprint" could become a new forensic tool, though it's not yet ready for the courtroom.

istockphoto.com
Hands on a keyboard

Researchers were able to correctly match bacterial DNA on keyboards and computer mice with their individual users. This bacterial "fingerprint" could become a new forensic tool, though it's not yet ready for the courtroom.

istockphoto.com

Most of the time, the DNA used for legal evidence is human DNA. But scientists in Colorado think DNA evidence from bacteria may someday finds its way into the courtroom.

Noah Fierer of the University of Colorado, Boulder, studies the bacteria that live on skin.

"Our bodies are covered in bacteria," says Fierer, "but most of these are harmless, and some of them may actually be beneficial. So it's nothing to be paranoid about." In fact, there are about a hundred different kinds of bacteria that typically grow on human skin.

And that gave Fierer an idea. "We leave this trail of bacteria everywhere we go, and the idea was could we use this trail to identify who had touched a given object or surface," he says.

The reason this bacterial trail could be used to identify someone is that we differ in the kinds of bacteria we carry around. Each of us has bacterial communities that are unique to us. And bacterial communities don't change very much over time.

So these communities could be used to identify someone.

Microbial 'CSI'

Let's say you wanted to find who has been using a particular office computer. Here's how it would work: "We could swab a keyboard key, for example, pull the bacterial DNA off that swab, and then identify all or nearly all of the bacteria that make up that community," says Fierer.

So that's what he did. He and his colleagues swabbed the individual keys from three personal computer keyboards, "and then matched those keys to the bacteria on the fingertips of the owners of the keyboard. And we showed that we could basically identify whose keyboard it was pretty well."

Fierer then tried a similar experiment with people's computer mice, and he could match a mouse to its owner. The findings appear in the current issue of Proceedings of the National Academy of Sciences.

In one final experiment, Fierer and his colleagues found that they could still perform an analysis of bacterial DNA two weeks after it had been left on a surface.

Fierer says he's already had some informal discussions with law-enforcement agencies about his bacterial ID techniques, and there's been interest in this approach. But Fierer's the first to say it's not ready for the courtroom. At least not yet.

"There's a lot of work we need to do to figure out how accurate it is and what are the limitations and so forth, but, yeah, it's encouraging. It does seem like we can actually take advantage of that uniqueness of our bacterial communities," he says.

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