Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 66,801 bioRxiv papers from 294,138 authors.

Reagent contamination can critically impact sequence-based microbiome analyses

By Susannah J. Salter, Michael J Cox, Elena M Turek, Szymon T Calus, William O Cookson, Miriam F Moffatt, Paul Turner, Julian Parkhill, Nick Loman, Alan W Walker

Posted 16 Jul 2014
bioRxiv DOI: 10.1101/007187 (published DOI: 10.1186/s12915-014-0087-z)

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. 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 is strongly advised.

Download data

  • Downloaded 5,112 times
  • Download rankings, all-time:
    • Site-wide: 412 out of 66,801
    • In molecular biology: 10 out of 2,133
  • Year to date:
    • Site-wide: 21,124 out of 66,801
  • Since beginning of last month:
    • Site-wide: 20,722 out of 66,801

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News