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Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations
Open accessAbstract
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.
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“Because the tumor microbiome has a relatively low biomass, contamination of the tumor samples with bacteria or bacterial DNA can be problematic (30, 31).”
From The human tumor microbiome is composed of tumor type–specific intracellular bacteria (2020) · cites this paper as [31]
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“Cell-free DNA was extracted from these plasma samples with extensive controls18,22 (Extended Data Figs. 9b–c), and processed for whole metagenomic sequencing by a limited set of users, using a single library preparation method47, in a single batch, in one deep-sequencing run.”
From RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach (2020) · cites this paper as [18]
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Metadata
- Authors
- Eisenhofer, R., Minich, J. J., Marotz, C., Cooper, A., Knight, R., & Weyrich, L. S.
- Affiliations
- Australian Research Council (AU)
- Scripps Institution of Oceanography (US)
- University of California San Diego (US)
- Corresponding author
- Eisenhofer, Raphael
- Venue
- Trends in Microbiology
- Publisher
- Elsevier BV
- Published
- 2019-02
- Volume
- 27
- Issue
- 2
- Pages
- 105-117
- ISSN
- 0966-842X (ISSN-L)
- OpenAlex
- W2903174799
- Cited by
- 1,146
- References
- 86
- Citations by year
- 2026: 234 · 2025: 149 · 2024: 112 · 2023: 150 · 2022: 153 · 2021: 163 · 2020: 120 · 2019: 62
- FWCI
- 8.61
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Trends in Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Funders
- Discovery Early Career Researcher Award (DE150101574)
- ARC (CE170100015)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- cross-contamination, experimental control
- MeSH terms
- DNA, Bacterial, Humans, Microbiological Techniques, Specimen Handling, Reproducibility of Results, Biomass, Metagenomics, High-Throughput Nucleotide Sequencing, DNA Contamination, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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