SEAN是一只程序猿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; inpolar 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]
在这个DNA技术成本相当低廉的时代，科学家正在为每个可以得到的样本的DNA进行测序。他们已经为蚊子体内、珊瑚粘液里、青蛙皮肤上、极地冰里甚至是漂浮在大气中的微生物进行了DNA测序。但是事实上，一些未经灭菌的实验室试剂和DNA提取设备会让一些不寻常的微生物群落不幸的被污染。一项发表在《BMC生物》杂志上的研究如是说。
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.
科学家们测序一个只有一种细菌的纯净样本。但是由于实验用的装置、试剂的不同，所在实验室的不同，他们得到结果中会包含高达270中不同的细菌菌株的DNA。许多受污染的微生物菌落可以在人的皮肤上被普遍地找到（也许是一名实验室的技术员身上？）。或者是在土壤或水中也很普遍。研究员说，这就可以解释一项最近的研究为什么会在肺癌组织样本中找到土壤里的细菌。另一项研究发现，婴儿的喉咙中的细菌随着他们年龄的增大而改变。但是这些研究员们说那项研究的细菌群落的改变不是因为年龄，而是因为随着时间的不同，用来测序的设备的品牌发生了变化造成的。
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.
这项研究的作者，阿伯丁大学的艾伦·沃克说，只有你正在使用的样本不是一种数量丰富的细菌的时候，污染才会是个问题。比如，如果你用粪便样本做研究，这个问题你或许就不会关心了，因为有足够的来自实际样本的DNA，它将抵消任何污染造成的问题。这是他给科学家们的建议？在实际的样本旁边，不要管已经有什么微生物潜伏在你的实验室会污染你的样本，只需要安心做你的测序工作就行了。
— Christopher Intagliata
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