Human DNA accidentally collected by scientists studying animals, plants, or microbes can reveal private information, raising ethical concerns for many researchers.
Everywhere they go, humans leave stray DNA. Police have used genetic sequences retrieved from cigarette butts and coffee cups to identify suspects; archaeologists have sifted DNA from cave dirt to identify ancient humans.
“I see this as a major ethics problem for the whole field,” says microbiome pioneer Rob Knight of the University of California, San Diego , who wrote an accompanying commentary. “We will have to completely rethink how we communicate to research subjects about the privacy risks of participating in microbiome research.”
In contrast, human geneticists Yukinori Okada and Yoshihiko Tomofuji of Osaka University and their colleagues set out from the start to see whether stray human sequences in their microbiome data posed a privacy problem. They had sequenced both the genomes and fecal microbiomes of 343 people to study how a person’s genes might correlate with and possibly influence their gut flora, and they wanted to be sure that if they shared any of their data, the donors would not be identifiable.
Knight says the analysis shows that the current methods microbiome researchers use to filter out human DNA and anonymize samples simply don’t work well enough. Researchers also need to re-evaluate how widely microbiome-derived sequences can be shared, he adds. “We are currently looking at withdrawing all the human metagenomic data sets we ever deposited, so we can redeposit only the sequences that positively match a microbe,” he says.
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