Microbiome 'fingerprints' could identify individuals

The communities of microbes living in and on the human body - known as the microbiome - differ enough between people that researchers can use them to tell one person from another in a population of hundreds.

By looking at the microbial DNA in samples from the skin, mouth, gut and vagina, scientists were able to generate unique codes for each person. The gut microbiome codes proved remarkably stable over time: 86 percent of people were identifiable nearly a year later.

'Linking a human DNA sample to a database of human DNA "fingerprints" is the basis for forensic genetics, which is now a decades-old field. We've shown that the same sort of linking is possible using DNA sequences from microbes inhabiting the human body - no human DNA required,' said author Dr Eric Franzosa, lead author of the study and research fellow at the Harvard Chan School of Public Health, Massachusetts, USA.

To generate the microbial fingerprints, the researchers developed a computer algorithm similar to ones that transmit information over the internet. The team applied their algorithm to a publicly available database produced from the Human Microbiome Project (HMP). The HMP took multiple samples from 242 people over a period ranging from 30 days up to one year.

Although the gut microbiome produced the strongest signatures, samples taken from other parts of the body still identified one third of people. The study, published in Proceedings of the National Academy of Sciences, also found that false matches were rare.

The team predicts that their identifying codes would only be unique in populations of around 700 people. 

A person's microbial features were, on the whole, worse at identifying people compared with using their cellular DNA. However, the ability to identify people by their microbiomes could raise concerns for people enrolled in microbiome research projects.

'This opens the door to connecting human microbiome samples between databases, which has the potential to expose sensitive subject information - for example, a sexually transmitted infection, detectable from the microbiome sample itself,' said Dr Franzosa.

Professor Curtis Huttenhower, senior author of the study, cautioned against undue worry, telling Nature it would be 'exceptionally challenging to do anything with the microbiome data in a single study'. Dr Amy McGuire, a bioethicist at Baylor College of Medicine in Houston, Texas also told the journal, 'I don’t think there should be premature panic over this.'