Lab contamination ruins many microbiome studies, researchers say

Lab contamination
Reagent and laboratory contamination can critically affect DNA sequence-based microbiome research, a study says.

New DNA sequencing technologies have greatly expanded our knowledge of the human microbiome - the teeming world of microorganisms that inhabit our bodies - yet a team of researchers now argues that many studies may be flawed because of contamination.

In a paper published Wednesday in the journal BMC Biology, researchers suggested that bacteria living on human skin, in the soil or in water have erroneously turned up in many microbiome studies, particularly those that seek to catalog sparse populations of microbes.

The contamination, the authors wrote, can occur during sample collection, preparation or during DNA sequencing because of tainted testing kits and reagents.

“This can critically impact study results, and we’re now advising caution to researchers studying microbiota,” said a statement from Alan Walker, a microbiologist who led the study at the Wellcome Trust Sanger Institute and who is now at the University of Aberdeen. Both institutions are in Britain.


Problems, according to the researchers, are more likely to crop up in samples where relatively few foreign microbes exist, such as in blood or the lungs.

Contamination is much less likely to be a problem in samples where large numbers of microbes exist, such as in feces, researchers said.

The paper is not the first to recognize the problem, although it did conclude that the risk of contamination was greater as the biomass of the sample became smaller.

The researchers tested their hunch by sequencing heavily diluted samples of Salmonella bongori bacteria and used a variety of testing kits. Heavily diluted samples revealed a number of other microbes not contained in the original sample, they found.


“Contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents and varies greatly in composition between different kits and kit batches,” the authors wrote.

“This contamination critically impacts results,” they wrote.

In order to flag false results, the researchers recommended the use of negative control samples. Such “blanks” do not contain specimen DNA but are processed along with samples that do.

If the negative control blanks reveal microbial DNA, it is because of contamination. If the same microbial DNA is picked up when the real sample is processed, it too is likely the result of contamination.

“Concurrent sequencing of negative control samples is strongly advised,” the authors wrote.

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