Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Susannah J Salter, Michael J Cox, Elena M Turek, Szymon T Calus, William O Cookson, Miriam F Moffatt, Paul Turner, Julian Parkhill, Nicholas J Loman, Alan W Walker

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Abstract

BACKGROUND: The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents.

RESULTS: In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination.

CONCLUSIONS: These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised.

Original languageEnglish
Article number87
JournalBMC Biology
Volume12
Issue number1
DOIs
Publication statusPublished - 12 Nov 2014

Keywords

  • contamination
  • microbiome
  • microbiota
  • metagenomics
  • 16S rRNA

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    Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014). Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biology, 12(1), [87]. https://doi.org/10.1186/s12915-014-0087-z