Contaminomics: Why Some Microbiome Studies May Be Wrong

Ed Yong in Not Exactly Rocket Science:

You’ve got a group of people with a mysterious disease, and you suspect that some microbe might be responsible. You collect blood and tissue samples, you extract the DNA from them using a commonly used kit of chemicals, and you sequence the lot. Eureka! You find that every patient has the same microbe—let’s say Bradyrhizobium, or Brady for short. Congratulations, you have discovered the cause of Disease X.

Don’t celebrate yet.

You run the exact same procedure on nothing more than a tube of sterile water and… you find Brady. The microbe wasn’t in your patients. It was in the chemical reagents you used in your experiments. It’s not the cause of Disease X; it’s a contaminant.

Versions of this story could be playing out in dozens of labs around the world. A team of scientists led by Susannah Salter and Alan Walker at the Wellcome Trust Sanger Institute has shown that DNA extraction kits, and other lab reagents commonly used in microbe studies, are almost always contaminated by low levels of microbial DNA.

Bradyrhizobium is a common culprit, but the team have identified a list of around 100 microbes whose DNA regularly turn up when sequencing supposedly “blank” tubes of water.

More here.