Journal article
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- Abstract:
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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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 1.5MB, Terms of use)
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- Publisher copy:
- 10.1186/s12915-014-0087-z
Authors
- Publisher:
- BioMed Central
- Journal:
- BMC Biology More from this journal
- Volume:
- 12
- Article number:
- 87
- Publication date:
- 2014-11-12
- Acceptance date:
- 2014-10-13
- DOI:
- EISSN:
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1741-7007
- Language:
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English
- Keywords:
- Pubs id:
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pubs:489832
- UUID:
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uuid:fc841c5a-c40f-413b-b3e7-31ff43201611
- Local pid:
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pubs:489832
- Source identifiers:
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489832
- Deposit date:
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2014-11-19
- ARK identifier:
Terms of use
- Copyright holder:
- Salter et al
- Copyright date:
- 2014
- Notes:
- © 2014 Salter et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Licence:
- CC Attribution (CC BY)
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