Laboratory contamination over time during low-biomass sample analysis

Laura S. Weyrich, Andrew G. Farrer, Raphael Eisenhofer, Luis A. Arriola, Jennifer Young, Caitlin A. Selway, Matilda Handsley-Davis, Christina J. Adler, Jimmy Breen, Alan Cooper

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

LanguageEnglish
Pages982-996
Number of pages15
JournalMolecular Ecology Resources
Volume19
Issue number4
DOIs
Publication statusPublished - 1 Jul 2019

Keywords

  • ancient DNA
  • contaminant
  • contamination
  • metagenomics
  • microbiome
  • microbiota

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Weyrich, L. S., Farrer, A. G., Eisenhofer, R., Arriola, L. A., Young, J., Selway, C. A., ... Cooper, A. (2019). Laboratory contamination over time during low-biomass sample analysis. Molecular Ecology Resources, 19(4), 982-996. https://doi.org/10.1111/1755-0998.13011
Weyrich, Laura S. ; Farrer, Andrew G. ; Eisenhofer, Raphael ; Arriola, Luis A. ; Young, Jennifer ; Selway, Caitlin A. ; Handsley-Davis, Matilda ; Adler, Christina J. ; Breen, Jimmy ; Cooper, Alan. / Laboratory contamination over time during low-biomass sample analysis. In: Molecular Ecology Resources. 2019 ; Vol. 19, No. 4. pp. 982-996.
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Weyrich, LS, Farrer, AG, Eisenhofer, R, Arriola, LA, Young, J, Selway, CA, Handsley-Davis, M, Adler, CJ, Breen, J & Cooper, A 2019, 'Laboratory contamination over time during low-biomass sample analysis', Molecular Ecology Resources, vol. 19, no. 4, pp. 982-996. https://doi.org/10.1111/1755-0998.13011

Laboratory contamination over time during low-biomass sample analysis. / Weyrich, Laura S.; Farrer, Andrew G.; Eisenhofer, Raphael; Arriola, Luis A.; Young, Jennifer; Selway, Caitlin A.; Handsley-Davis, Matilda; Adler, Christina J.; Breen, Jimmy; Cooper, Alan.

In: Molecular Ecology Resources, Vol. 19, No. 4, 01.07.2019, p. 982-996.

Research output: Contribution to journalArticle

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Weyrich LS, Farrer AG, Eisenhofer R, Arriola LA, Young J, Selway CA et al. Laboratory contamination over time during low-biomass sample analysis. Molecular Ecology Resources. 2019 Jul 1;19(4):982-996. https://doi.org/10.1111/1755-0998.13011