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

BMC Biology

Research Article

Nicholas J Loman¹  Szymon T Calus¹  William O Cookson²  Elena M Turek²  Miriam F Moffatt²  Michael J Cox²  Julian Parkhill³  Susannah J Salter³  Alan W Walker⁴  Paul Turner⁵ 

[1] Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK;Molecular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK;Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK;Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK;Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK;Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand;Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK;

关键词: Contamination;    Microbiome;    Microbiota;    Metagenomics;    16S rRNA;   

DOI  :  10.1186/s12915-014-0087-z

 received in 2014-07-15, accepted in 2014-10-13,  发布年份 2014

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Salter et al.; licensee BioMed Central Ltd. 2014