Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

Raphael Eisenhofer; Jeremiah J Minich; Clarisse Marotz; Alan Cooper; Rob Knight; Laura S Weyrich

doi:10.1016/j.tim.2018.11.003

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

Trends Microbiol. 2019 Feb;27(2):105-117. doi: 10.1016/j.tim.2018.11.003. Epub 2018 Nov 26.

Authors

Raphael Eisenhofer¹, Jeremiah J Minich², Clarisse Marotz³, Alan Cooper⁴, Rob Knight⁵, Laura S Weyrich⁴

Affiliations

¹ Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA, Australia. Electronic address: raph.eisenhofer@gmail.com.
² Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA, USA.
³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
⁴ Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA, Australia.
⁵ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

PMID: 30497919
DOI: 10.1016/j.tim.2018.11.003

Abstract

Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass samples. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.

Keywords: DNA contamination; laboratory contamination; low biomass; methodology; microbiome; microbiota.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Biomass*
DNA Contamination*
DNA, Bacterial / analysis
DNA, Bacterial / genetics
High-Throughput Nucleotide Sequencing
Humans
Metagenomics
Microbiological Techniques / methods
Microbiological Techniques / standards
Microbiota / genetics*
Reproducibility of Results
Specimen Handling

Substances

DNA, Bacterial