Many microbiome studies may be flawed, a new study points out. Studies may under report contamination of lab equipment by microorganisms in the laboratory environment, and in contaminated DNA testing kits. These results may account for some studies where scientists find microbiomes in unusual places.
This new study was published in the journal BMC Biology, and was led by the Wellcome Trust Sanger Institute.
Since the introduction of cheap DNA testing kits, microbiome research has exploded. Recently, scientists have looked at the DNA and bacterial makeup of everything from placenta to the colon. Researchers are using these studies to identify possible markers for disease, including cancer and depression. However, this new study shows that some of these microbiome studies may be inaccurate because some of the testing kits already contain microbiomes on them when they start. Researchers may get different results depending on which brand of testing kit they use, or what laboratory they are in. The researchers found over 270 different strains of bacteria in their control samples. If there had been no contamination present, there should only have been one strain of bacteria present.
"Recent advances in DNA sequencing technology - which allow extraordinary depth of sequencing - are being used by researchers to analyse extremely sparse microbial populations. What we have now shown is that these types of samples are susceptible to contaminant DNA from any source, whether it is at the time of collection, from handling samples, or during the extraction or amplification process. This can critically impact study results, and we're now advising caution to researchers studying microbiota in low biomass environments," said Dr. Alan Walker, the lead author of the study.
These researchers also measured how much of an effect microbiome contamination had on different samples of differing biomass. They found that the higher the biomass of a sample, the less impact contamination had on the results. For example, feces, where a lot of tissue is sampled, was less likely to be as contaminated as samples where there is only a small amount of the sample, such as from the lungs.
To lower the risk of contamination affecting results, the researchers suggested that scientists should run a control test to determine what biomarkers exist in the testing kits.
