Journal
BMC BIOLOGY
Volume 12, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s12915-014-0087-z
Keywords
Contamination; Microbiome; Microbiota; Metagenomics; 16S rRNA
Categories
Funding
- Wellcome Trust [098051, 083735/Z/07/Z]
- Wellcome Trust Centre for Respiratory Infection Basic Science Fellowship
- National Institute for Health Research (NIHR)
- Medical Research Council Special Training Fellowship in Biomedical Informatics
- Scottish Government Rural and Environmental Science and Analysis Service (RESAS)
- Wellcome Trust [096964/Z/11/Z] Funding Source: Wellcome Trust
- MRC [MR/J014370/1, MR/L015080/1] Funding Source: UKRI
- Medical Research Council [MR/J014370/1, MR/L015080/1] Funding Source: researchfish
- Wellcome Trust [096964/Z/11/Z] Funding Source: researchfish
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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.
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