Researchers from the Harvard T.H. Chan School of Public Health in Boston, MA, have shown in a new study that the microbial communities found inside and on the bodies of individuals – referred to as the microbiome – have the potential to uniquely identify individuals.
The study, published in Proceedings of the National Academy of Sciences, is the first to demonstrate the feasibility of using personal microbiome data to identify individuals, although it also suggests that there may be privacy concerns for the participants of human microbiome research projects.
Lead author Eric Franzosa, a research fellow in the Department of Biostatistics at Harvard Chan, states that, for decades, the field of forensic genetics has been based on linking human DNA samples to a database of human DNA “fingerprints.”
“We’ve shown that the same sort of linking is possible using DNA sequences from microbes inhabiting the human body – no human DNA required,” Franzosa says.
“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.”
In an average human body, there are on average 10 times more bacteria than human cells. These bacteria play a prominent role in maintaining health by producing vitamins, breaking down food, supporting the immune system and producing anti-inflammatory compounds.
When the microbiome is disrupted, health problems such as bowel inflammation can occur. Recent studies published in the past 6 months have also made associations between the microbiome, particularly in the gut, with conditions such as Parkinson’s disease, food allergies and asthma and with the production of serotonin.
For the study, the researchers analyzed data obtained from the Human Microbiome Project. They surveyed microbes from the saliva, skin, stool and other body sites of 242 participants for over a month.
With the help of an adapted computer science algorithm, the researchers created specific “codes” for each individual. These codes were constructed by combining stable and distinguishing sequence features from the microbiome samples.
These individual-specific codes were then compared with microbiome samples obtained from the same individuals at follow-up visits, as well as with samples collected from independent groups of individuals.
The researchers found that not only were the codes unique among hundreds of individuals, but that a significant number of them remained stable throughout a sampling period of 1 year. Codes constructed using data obtained from the gut were particularly stable, with over 80% remaining identifiable up to a year after the initial sampling period.
Senior author Curtis Huttenhower, an associate professor of computational biology at Harvard Chan, states that it is important for researchers to know it is theoretically possible for data privacy issues to arise with microbial DNA, even if the potential is quite low. The study demonstrates samples from a variety of body sites can be linked to individuals without any additional identifying information.
However, he believes that another aspect of their research is more interesting:
“Perhaps even more exciting are the implications of the study for microbial ecology, since it suggests our unique microbial residents are tuned to the environment of our body – our genetics, diet and developmental history – in such a way that they stick with us and help to fend off less-friendly microbial invaders over time.”
“Although the populations considered here were small relative to real-world human communities (20-50 individuals), we estimate that this lower bound on microbiome-driven identifiability scales to at least hundreds of individuals, and this population size is representative of the cohorts currently used in microbiome research,” the authors conclude.
The research was partly funded by the National Institutes of Health (NIH).
Medical News Today previously ran a Spotlight feature on how the gut microbiome affects our health, finding that a more diverse microbiome is better for health and that there are several ways in which gut bacteria can be altered.