Microbiome Studies Contaminated By Sequencing Supplies

Non-sterile lab reagents and DNA extraction kits add their own assortment of DNA to microbiome samples. Christopher Intagliata reports. November 11, 2014 | |

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, and ; in ; even . 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 . [Susannah J Salter et al.: ]

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 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 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.]