How your microbiome can put you at the scene of the crime

ByKai KupferschmidtMar. 8, 2016 , 9:45 AM

One morning last summer, evolutionary biologist Jose Lopez was having coffee on the back porch of his house in Hollywood, Florida, when two burglars climbed in through a front window and did what home invaders usually do: They rifled through drawers, disconnected the TV to carry it off, and even opened the fridge to have a Coke.

This wasn’t an ordinary break-in, however. The invaders were employees of the local sheriff’s office, and the burglary was part of a science project. Later, forensics experts swooped in to swab down surfaces and handles in the house. In a laboratory at the University of Chicago (UC) in Illinois, colleagues of Lopez’s isolated DNA from these swabs and fished out parts of one particular stretch named 16S rDNA—a sequence that is distinctive for almost every bacterial species. By amplifying and sequencing these bits, the scientists were able to identify hundreds of different species in each swab.

After eliminating the species left by the house’s legitimate residents—including a cat—they were left with a new kind of physical evidence: the microbial DNA deposited by the thieves as they moved through the rooms. Because the mix of species and strains in a person’s microbiome is highly individual, such molecular signatures might be used to place someone at a crime scene, says Jack Gilbert, a microbial ecologist at UC. And because the microbiome varies by gender, age, and lifestyle, the data could also be used to build up a picture of a suspect.

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The field is in its infancy; so far, the only crime it has helped solve occurred on the hit TV show CSI: Miami. Some scientists are skeptical that microbial signatures are individual enough to be used as evidence in court. “I think we are very far from using the microbiome in forensic analysis. If it will ever be used,” says microbiologist Jacques Ravel of the University of Maryland, Baltimore. Others are more optimistic. “We have enough data to suggest it is well worth exploring,” says David Relman, who studies human and animal microbiomes at Stanford University in Palo Alto, California.

Read more of our special package that examines the hurdles and advances in the field of forensics

Hopes that microbiomescould help solve crimes date from a study published in 2010 in the Proceedings of the National Academy of Sciences, which showed that bacterial DNA recovered from computer keyboards matched the microbiomes found on their owners’ fingertips. The authors also sampled bacteria from nine computer mice and used the results to pick the owners out of a database of 270 microbiomes. “This was the first paper to demonstrate that people leave a highly unique and identifiable signature,” Gilbert says.

Adding to the microbiome’s appeal for forensics, people shed bacteria constantly and indiscriminately. “You’re shedding them from your face, spitting them out from your mouth, breathing them out though your nose,” Gilbert says. They aren’t confined by gloves or clothes. “Your trousers or your pants are like a loose fish net material to bacteria. As soon as you sit down, your bottom or your vaginal microbiota is expelled onto that surface and it is actually reasonably persistent until the next person sits down,” Gilbert says. In a 2015 paper, scientists measured the airborne bacteria surrounding volunteers in a sanitized chamber and were able to identify some of the subjects by their microbial cloud.

All told, researchers have sampled microbiomes from thousands of people, mostly volunteers from Europe and the United States, and found that the relative abundances of microbial species are highly individual. Even identical twins can be told apart. One reason our microbiome is so highly personal is that it’s partly determined by our genome and immune system. Chance plays a role as well. In the first 3 or 4 years of life, humans seem to pick up a unique set of bacteria from the vast natural diversity they’re exposed to; that mix remains fairly stable all their lives, says Peer Bork, a computational biologist at the European Molecular Biology Laboratory in Heidelberg, Germany.

Yet the question is whether these signatures can be used to identify a person beyond a reasonable doubt, as human DNA evidence can. Bork thinks that will be possible, but not with the 16S rDNA technique alone, because it mostly picks up differences between bacterial species. Instead, he thinks investigators need to fully sequence all the DNA swabbed from a crime scene and from suspects’ microbiomes, to detect small differences between strains of the same species. “You and I both have E. coli, but I have a slightly different strain than you,” Bork says. “We carry about a thousand different species in the micro- biome. If we look at differences in all of them, we may well be able to distinguish 8 billion people.” So far, Bork’s group has studied about 3500 individuals using this strategy; all of them were unique. But because it entails extensive sequencing, this approach comes with a higher price tag.

Another problem is that both individual bacteria and the composition of microbial communities change over time. The signature a murderer left at a crime scene a decade ago may not exactly match his microbial cloud today. Moving to a different country changes the microbiome as well, and antibiotics can radically alter it. Smart criminals might pop a few pills before they strike, “like criminals who used to burn their fingertips with acid and other unpleasant techniques,” says Rob Knight of the University of California, San Diego, one of the leaders of the new field.

To help solve crimes, forensic analysts would need the equivalent of a fingerprint library: a database of known microbiome profiles to which they can compare evidence from a crime scene. “We would need 8 billion stool or skin samples,” Bork says. “I’m not sure how practical that is.” But Gilbert doesn’t think that’s a big problem. He says such databases could be built up the same way they have been for fingerprints: gradually, starting with convicted criminals.

Even if microbiologists can’t pinpoint one particular culprit, a microbiome left at a crime scene may hold important clues. Is the perpetrator a man or a woman? Does he smoke? Where does she live? “Unlike fibers or fragments of hair, the microbiome contains an awful lot of information,” Gilbert says. For instance, a small study he did with collaborators in Shanghai, China, found big differences between the skin microbiomes of people living in urban, suburban, and rural areas.

In the fake break-in, Gilbert compared the signatures of the two intruders with a database of a few thousand people that he has built up; based on the relative abundance of particular taxonomic groups, he predicted that one of the burglars had at least 10 alcoholic drinks a week and that the other was on migraine medication. He was right on both counts. “When I heard that, I was in shock,” says George Duncan, a DNA expert at the Broward County Sherriff’s office who had organized the burglary. These kinds of leads could be very valuable to police, he says.

Bork notes, however, that “at the moment many of these associations are very shaky.” For instance, two groups have reported that the microbiomes of diabetes patients can be distinguished from that of nondiabetics. But a careful analysis by Bork’s group, published in Nature in December 2015, showed that what scientists had detected was not a signature from the disease, but from the common diabetes drug metformin.

Gilbert is trying to improve his database by recruiting more people in Chicago and Florida with jobs or lifestyles that leave a particularly strong mark on the micro- biome, such as bakers, farmers, vegetarians, and vegans. To help the field along further, Rhonda Roby of the J. Craig Venter Institute in Rockville, Maryland, has received a grant of more than $900,000 from the National Institute of Justice to build a micro- biome database containing thousands or even tens of thousands of samples for the forensics community.

One thing is for sure, Ravel says: Scientists will need to tread carefully. Junk science has landed innocent people in jail in the past; the last thing microbiologists should do is add another flawed technique to the forensic arsenal, he says. “You don’t want to start accusing and messing up the lives of many people just because they have a microbiome similar to the one found at the crime scene.”

Posted in:

  • Biology
  • Forensics

DOI: 10.1126/science.aaf4159