ArticleBMC biology2014
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
Article in BMC biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,930 papers, 1 of them a synthesis that pooled it.
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Who cites it
1,930 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- The role of the respiratory microbiome in acute and chronic respiratory diseases.Nature reviews. Microbiology · 2026Review
- Microbiome-based diagnostic biomarkers in pancreatic ductal adenocarcinoma: Current evidence and translational challenges (Review).Oncology letters · 2026Review
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- The Microbiome in Glioblastoma: Mechanisms, Tumor-Immune Interactions, and Translational Perspectives.MicrobiologyOpen · 2026Review
- Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.Current microbiology · 2026Review
- Diagnostic Yield and Incremental Value of 16S rRNA Gene PCR and Sequencing on Excised Heart-Valve Tissue in Infective Endocarditis: A Systematic Review and Meta-Analysis.Diagnostics (Basel, Switzerland) · 2026Review
- Pathogen-oriented mNGS is not equivalent to microbiome profiling: interpreting BALF mNGS diversity in ARDS.Journal of intensive care · 2026Article
- Cecal microbiota-host phenotype associations in young White Leghorn and Silky Fowl chickens.Poultry science · 2026Article
- The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.Molecular and cellular pediatrics · 2026Review
1,870 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
backgroundThe 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.
resultsIn 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.
conclusionsThese 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.
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