The more than 100 trillion microbes we host – the human microbiota – can identify us as individuals much like a fingerprint, a new study by Harvard TH Chan School of Public Health reveals. It seems that these personal microorganisms have distinguishing features that can potentially be used to identify us over time. Published in the journal PNAS, this research is the first to rigorously show that identifying people from their microbiome data is feasible.
Using publicly available data produced through the Human Microbiome Project (HMP), researchers examined microbes from 242 individuals over a 12-month period. Then, they applied an adapted version of a classic computer science algorithm to scan the microbial genetic code and search through different sequence features for patterns that are unique to each individual. To do so, they combined stable and distinguishing sequence features from the individuals’ initial microbiome samples and compared them both to samples from the same individuals collected at follow-up visits and samples collected from control group individuals.
Researchers found that the ‘codes’ were unique among hundreds of participants and that, also, a number of them (more than 80%) remained stable over the sampling period of one year. In some ways, it could be said they were able to identify “microbiome fingerprints”, because similarly to what happens with the genome, in the case of the microbiome, there are many aspects that are the same for many people but the existing differences are enough to characterise each individual.
“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. 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,” lead author Eric Franzosa, research fellow at the Department of Biostatistics at Harvard Chan, said in a press release.
Similarly to forensics genetics, which use small differences in the human genome to identify individuals, Franzosa and his colleagues believe the same method could be applicable to microbiome information in the cases in which human DNA is not available or has become too deteriorated. It may be, then, that some day, microbiome sequencing will be a useful tool in criminal investigations.
The authors highlight that the study also has some implications for microbial ecology research, as it suggests our unique microbial residents are tuned into our history and the environment of our body – namely our genetics, diet and developmental history – in such a way that they stick with us and help combat invaders over time.