Imperial College London

DrMichaelCox

Faculty of MedicineNational Heart & Lung Institute

Research Associate
 
 
 
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Contact

 

+44 (0)20 7594 7974michael.cox1 Website

 
 
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Location

 

413Guy Scadding BuildingRoyal Brompton Campus

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Summary

 

Publications

Citation

BibTex format

@article{Salter:2014:10.1186/s12915-014-0087-z,
author = {Salter, SJ and Cox, MJ and Turek, EM and Calus, ST and Cookson, WO and Moffatt, MF and Turner, P and Parkhill, J and Loman, NJ and Walker, AW},
doi = {10.1186/s12915-014-0087-z},
journal = {BMC Biology},
title = {Reagent and laboratory contamination can critically impact sequence-based microbiome analyses},
url = {http://dx.doi.org/10.1186/s12915-014-0087-z},
volume = {12},
year = {2014}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - BackgroundThe 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.ResultsIn 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.ConclusionsThese 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.
AU - Salter,SJ
AU - Cox,MJ
AU - Turek,EM
AU - Calus,ST
AU - Cookson,WO
AU - Moffatt,MF
AU - Turner,P
AU - Parkhill,J
AU - Loman,NJ
AU - Walker,AW
DO - 10.1186/s12915-014-0087-z
PY - 2014///
SN - 1741-7007
TI - Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
T2 - BMC Biology
UR - http://dx.doi.org/10.1186/s12915-014-0087-z
UR - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000345876100001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR - https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-014-0087-z
UR - http://hdl.handle.net/10044/1/72529
VL - 12
ER -