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More research is needed, but looking at the "microbial signature" of a criminal definitely has potential. From Science (American Association for the Advancement of Science):

Bacteria on pubic hair could be used to identify rapists

When it comes to identifying a rapist, one of the main pieces of evidence police analyze are pubic hairs found at the crime scene. But most of these hairs are missing their roots and thus don’t harbor enough DNA for a proper match. Now, a new study suggests there may be a better way to finger the criminal: Look at the bacteria he left behind.

In addition to hair, police have relied heavily on semen samples to identify potential rapists, notes Silvana Tridico, a forensic biologist at Murdoch University in Perth, Australia. But criminals have gotten wise to genetic testing, she says, and are increasingly wearing condoms, which they take with them after assaults. She hoped to find a way to get around this problem by comparing bacteria that are present in the pubic hairs of the victim and suspects and then creating a microbial fingerprint that could nail the culprit.

Tridico and colleagues asked seven individuals—two of whom were living together—to collect their scalp and pubic hair for 5 months. The researchers then analyzed these samples in the lab, looking for bacterial populations present after 2 and 5 months. The scalp hair showed that 50 different varieties of microbes in males and 55 in females are found in this part of the body, but many of the microbes that were found were not specific to the individual carrying them. The pubic hair bacteria, however, turned out to be more distinct; in addition, each individual’s “personal” pubic bacteria stayed roughly the same during the 5 months. More kinds of bacteria live in these hairs: approximately 73 in males and 76 in females. A larger combination of different bacteria means it is more likely for people to carry a unique microbial signature on them, Tridico says.

Although each person’s pubic hair bacteria were distinct, the couple who were living together had greater similarity of bacteria on their pubic hairs at 5 months than detected after 2 months. The couple later revealed that they had sexual intercourse 18 hours before the collection of their hairs, the researchers report online today in Investigative Genetics.

Because the study included only one couple who were living together and only seven participants in total, the results are “far from conclusive,” Tridico cautions. However, the findings are encouraging, she says, and show that “it may be possible to differentiate between individuals on the basis of their bacteria.”

Max Houck, a lead forensic scientist at Consolidated Forensic Laboratory, a government organization based in Washington, D.C., agrees. But he also points out that it might be more difficult to use this method if there has been previous sexual contact between the victim and the subject, in the case of abusive ex-spouses, for example. “Human pubic hairs could be of potentially significant use in cases where the victim and subject have not had previous sexual contact.”