ArticleGut pathogens2016
Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples.
Article in Gut pathogens, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 315 papers, 2 of them syntheses that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
315 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations.Nature communications · 2023Pooled it
- Concordance of molecular microbiology and conventional culture techniques for infected diabetic foot ulcer management.Diabetic medicine : a journal of the British Diabetic Association · 2025Trial
- Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.PloS one · 2021Trial
- Integrating multiplex digital PCR and long-read sequencing toward standardized genome integrity and purity characterization of rAAV9.Molecular therapy. Advances · 2026Article
- Methane is an important selection factor in microbial community assembly along the Greenland Ice Sheet margin.Applied and environmental microbiology · 2026Article
- The role of the respiratory microbiome in acute and chronic respiratory diseases.Nature reviews. Microbiology · 2026Review
- The Microbiome in Glioblastoma: Mechanisms, Tumor-Immune Interactions, and Translational Perspectives.MicrobiologyOpen · 2026Review
- Impact of Infant Feeding Mode on Gut Microbiome Composition in Early Life: Evidence from an Egyptian Cohort.Scientific reports · 2026Article
- Unfolding the Semen Microbiota: Implications for Male Infertility.Biomedicines · 2026Review
- Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.Current opinion in ophthalmology · 2026Review
- NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.BMC bioinformatics · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- The Phylum Fusobacteriota Is Associated with Colorectal Cancer-Specific Mortality: Results from the Translational Research Program in Cancer Differences across Populations.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026Article
- Molecular Characterization of the Middle Ear Microbiome in Pediatric Otitis Media with Effusion: Diagnostic and Clinical Implications.Journal of clinical medicine · 2026Review
- Habitat Type and Locality Structure the Midgut Microbiota of Aedes albopictus.Microbial ecology · 2026Article
- The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.Animal microbiome · 2026Article
- The Equine Reproductive Microbiota: Composition, Dynamics, Dysbiosis, and Implications for Fertility in Mares and Stallions.Animals : an open access journal from MDPI · 2026Review
- Evaluating long-read metagenomics for bloodstream infection diagnostics: a pilot study from a Thai Tertiary Hospital.Scientific reports · 2026Article
- DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants.BMC bioinformatics · 2026Article
255 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe advent and use of highly sensitive molecular biology techniques to explore the microbiota and microbiome in environmental and tissue samples have detected the presence of contaminating microbial DNA within reagents. These microbial DNA contaminants may distort taxonomic distributions and relative frequencies in microbial datasets, as well as contribute to erroneous interpretations and identifications.
resultsWe herein report on the occurrence of bacterial DNA contamination within commonly used DNA extraction kits and PCR reagents and the effect of these contaminates on data interpretation. When compared to previous reports, we identified an additional 88 bacterial genera as potential contaminants of molecular biology grade reagents, bringing the total number of known contaminating microbes to 181 genera. Many of the contaminants detected are considered normal inhabitants of the human gastrointestinal tract and the environment and are often indistinguishable from those genuinely present in the sample.
conclusionsLaboratories working on bacterial populations need to define contaminants present in all extraction kits and reagents used in the processing of DNA. Any unusual and/or unexpected findings need to be viewed as possible contamination as opposed to unique findings.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.