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Type: Journal article
Title: Laboratory contamination over time during low-biomass sample analysis
Author: Weyrich, L.S.
Farrer, A.G.
Eisenhofer, R.
Arriola, L.A.
Young, J.
Selway, C.A.
Handsley-Davis, M.
Adler, C.J.
Breen, J.
Cooper, A.
Citation: Molecular ecology resources, 2019; 19(4):982-996
Publisher: Wiley Online Library
Issue Date: 2019
ISSN: 1755-0998
Statement of
Laura S. Weyrich, Andrew G. Farrer, Raphael Eisenhofer, Luis A. Arriola Jennifer Young, Caitlin A. Selway, Matilda Handsley‐Davis, Christina J. Adler James Breen, Alan Cooper
Abstract: Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.
Keywords: ancient DNA; contaminant; contamination; metagenomics; microbiome; microbiota
Rights: © 2019 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
RMID: 0030111797
DOI: 10.1111/1755-0998.13011
Grant ID:
Appears in Collections:Environment Institute publications

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