科学美国人60秒:Microbiome Studies Contaminated By Sequencing Supplies

In this age of cheap DNA technology, scientists are sequencing every sample they can get their hands on. They've ID'd the microbes in mosquito guts, coral mucus and frog skin; in polar ice; even floating in the Earth's atmosphere. But it turns out some of the bugs reported to belong to those unusual microbiomes could unfortunately be contaminants, from non-sterile lab reagents and DNA extraction kits. So says a study in the journal BMC Biology. [Susannah J Salter et al.: Reagent and laboratory contamination can critically impact sequence-based microbiome analyses]

Researchers sequenced a pure sample of just one type of bacteria. But depending which kit they used, which reagents, which lab, their results contained DNA from up to 270 different bacterial strains. Many of those contaminating strains are commonly found on human skin…(a lab technician's, maybe?). Or in soil or water. Which could explain why one recent study turned up soil bacteria in samples of breast cancer tissue, the researchers say. Another study found that infants' throat bacteria change as they get older. But these researchers say the changing bacterial communities in that study were due not to age—but to changing the brand of DNA kit over time.

study author Alan Walker, of the University of Aberdeen, says contamination is only a problem if you're working with samples that aren't already rich in bacteria. "If you're doing fecal work, for example, this probably doesn't concern you, because there's enough DNA coming from the actual sample that it'll drown out any of the background contamination." His recommendation for scientists? Alongside the actual samples, try sequencing nothing…to see what sort of shadow microbiome is already lurking in your lab.

-- Christopher Intagliata

[The above text is a transcript of this podcast.]