Contaminated samples point the finger at the wrong suspects

Some studies on the relationship between microbes and human health may be producing incorrect results due to lab contamination, according to a study.

Bacteria that live inside our bodies – known as the microbiome – are a hot topic in biomedical science, with many studies claiming they play central roles in health and disease.

Researchers from Imperial College London, the Wellcome Trust Sanger Institute, and the University of Birmingham identified about 100 microbes whose DNA often crops up in samples that are supposed to be blank, with no microbes or DNA present.

The study, published in the journal BMC Biology, went further to point out 20 published papers that ascribe roles to organisms that commonly cause contamination, which the authors suggest may not have been present in the original samples.

“It was really an observation that we started to see bacteria appearing in our samples you wouldn’t expect to find in human samples,” says Dr Michael Cox, co-author of the study from the National Heart and Lung Institute at Imperial. “We talked to some collaborators at other universities, and they were seeing a similar thing. So we decided to get together to put together a collaborative experiment that revealed where these organisms were coming from.”

The experiment that the researchers came up with was to take an organism of interest and dilute it so that there was very little of it left in the sample. “As we diluted out the organism that we cultured, many more other organisms started to appear and it turned out that the actual sources of these were the DNA extraction kits that were being used,” Cox said.

“It’s quite well established in some fields that you get contamination in these samples. This does not seem to have been recognised by many people working on the human microbiome, maybe because they are not aware of the prior publications.”

When researchers work with samples that contain a large number of microbes, such as faecal samples, the microbes are likely to overcome the effect of the contaminants. But with samples that contain fewer microbes, such as those from the spinal fluid or the lungs, contamination is more likely to be an issue.

“It will be difficult to eliminate all contamination, but the majority of the problem can be overcome with good controls and experimental design,” Cox said. “For example, when collecting samples from inside the airways, researchers should collect saline used to rinse the bronchoscope before it goes into the patient. Then bacteria found in the rinse can be discounted from the analysis.”

The Wellcome Trust, National Health Service, National Institute for Health Research, Department of Health and the Scottish Government Rural and Environmental Science and Analysis Service funded the work.

Reference: Salter, S. J. et al. (2014) 'Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.' BMC Biology. [Online] 12 (87).