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 and Susannah:2014:10.1101/007187,
author = {Salter and Susannah, Cox and Michael, J Turek and Elena, M Calus and Szymon, T Cookson and William, O Moffatt and Miriam, F Turner and Paul, Parkhill and Julian, Loman and Nick, Walker and Alan, W},
doi = {10.1101/007187},
journal = {bioRxiv},
title = {Reagent contamination can critically impact sequence-based microbiome analyses},
url = {http://dx.doi.org/10.1101/007187},
year = {2014}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - Susannah Salter1,7 (sb18{at}sanger.ac.uk), Michael J Cox2 (michael.cox1{at}imperial.ac.uk), Elena M Turek2 (elena.turek11{at}imperial.ac.uk), Szymon T Calus3 (s.t.calus{at}bham.ac.uk), William O Cookson2 (w.cookson{at}imperial.ac.uk), Miriam F Moffatt2 (m.moffatt{at}imperial.ac.uk), Paul Turner4 (pault{at}tropmedres.ac), Julian Parkhill5 (parkhill{at}sanger.ac.uk), Nick Loman3 (n.j.loman{at}bham.ac.uk) and Alan W Walker6 (alan.walker{at}abdn.ac.uk) 1 Wellcome Trust Sanger Institute; 2 Molecular Genetics and Genomics, National Heart and Lung Institute, Imperial College London; 3 Institute of Microbiology and Infection, University of Birmingham; 4 Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford; 5 Pathogen Genomics, Wellcome Trust Sanger Institute; 6 Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen ↵ Corresponding author; email: sb18{at}sanger.ac.uk AbstractThe 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 i
AU - Salter
AU - Susannah,Cox
AU - Michael,J Turek
AU - Elena,M Calus
AU - Szymon,T Cookson
AU - William,O Moffatt
AU - Miriam,F Turner
AU - Paul,Parkhill
AU - Julian,Loman
AU - Nick,Walker
AU - Alan,W
DO - 10.1101/007187
PY - 2014///
TI - Reagent contamination can critically impact sequence-based microbiome analyses
T2 - bioRxiv
UR - http://dx.doi.org/10.1101/007187
UR - http://biorxiv.org/content/early/2014/07/16/007187.abstract
ER -