RT Journal Article
SR Electronic
T1 Reagent contamination can critically impact sequence-based microbiome analyses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 007187
DO 10.1101/007187
A1 Susannah J Salter
A1 Michael J Cox
A1 Elena M Turek
A1 Szymon T Calus
A1 William O Cookson
A1 Miriam F Moffatt
A1 Paul Turner
A1 Julian Parkhill
A1 Nick Loman
A1 Alan W Walker
YR 2014
UL http://biorxiv.org/content/early/2014/07/16/007187.abstract
AB 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. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, 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. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.