Cited by 1,146Genomics and Phylogenetic StudiesGut microbiota and healthMicrobial Community Ecology and Physiology

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Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

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Eisenhofer, Raphael, Minich, Jeremiah J., Marotz, Clarisse, Cooper, Alan, Knight, Rob, Weyrich, Laura S.·2019·Trends in Microbiology

DOI 10.1016/j.tim.2018.11.003

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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.

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Additional file 3 of Using strain-resolved analysis to identify contamination in metagenomics data
Lou, Y. C., Hoff, J., Olm, M. R., West-Roberts, J. A., Diamond, S., Firek, B., Morowitz, M. J., & Banfield, J. F. (2023) · Figshare · doi:10.6084/m9.figshare.22613114
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Additional file 5 of Differences in airway microbiome and metabolome of single lung transplant recipients
Sharma, N., Vestal, G. D., Wille, K. M., Patel, K., Cheng, F., Tipparaju, S. M., Tousif, S., Banday, M. M., Xu, X., Wilson, L. S., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12262604
Additional file 4 of Differences in airway microbiome and metabolome of single lung transplant recipients
Sharma, N., Vestal, G. D., Wille, K. M., Patel, K., Cheng, F., Tipparaju, S. M., Tousif, S., Banday, M. M., Xu, X., Wilson, L. S., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12262595
Additional file 8 of Differences in airway microbiome and metabolome of single lung transplant recipients
Sharma, N., Vestal, G. D., Wille, K. M., Patel, K., Cheng, F., Tipparaju, S. M., Tousif, S., Banday, M. M., Xu, X., Wilson, L. S., et al. (2020) · Figshare · doi:10.6084/m9.figshare.12262628
Additional file 2 of Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens
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Additional file 1 of Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods
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Thakkar, K., Richard, C., Fu, H., Simpson, B. S. S., Cha, H., Augustine, M., Coulton, A., Castro, A., Veerian, S., AbdulJabbar, K., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4820266
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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
ORCID: Eisenhofer, Raphael
Minich, Jeremiah J.
Marotz, Clarisse
Cooper, Alan
Knight, Rob
Venue: Trends in Microbiology
Publisher: Elsevier BV
Published: 2019-02
Volume: 27
Issue: 2
Pages: 105-117
ISSN: 0966-842X (ISSN-L)
DOI: 10.1016/j.tim.2018.11.003
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
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
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

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