ArticleMolecular ecology resources2019
Laboratory contamination over time during low-biomass sample analysis.
Article in Molecular ecology resources, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
131 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Modulation of the response to immunotherapy in triple-negative breast cancer: the role of the microbiota and microbial metabolites in the tumor microenvironment.Gut microbes · 2026Review
- Systematic quantification and removal of host DNA contamination in 16S rRNA gene sequencing.Quantitative biology (Beijing, China) · 2026Article
- The role of the respiratory microbiome in acute and chronic respiratory diseases.Nature reviews. Microbiology · 2026Review
- Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.American journal of biological anthropology · 2026Article
- Mitochondria Meet the Lung Microbiome: A Bidirectional Dialogue in Inflammation and Respiratory Diseases.Biomedicines · 2026Review
- Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.Journal of bacteriology · 2026Review
- Spatial Heterogeneity of Intratumoral Microbiota and Its Roles in Tumor-Microbiota Interactions and Therapeutic Implications.Pathogens (Basel, Switzerland) · 2026Review
- Comprehensive microbiome profiling reveals mucosal microbiome heterogeneity in patients with left- and right-sided colorectal neoplasia.Cancer biology & medicine · 2026Article
- A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.Molecular ecology resources · 2026Article
- Spatial and temporal patterns of public transit aerobiomes.Microbiome · 2026Article
- Impact of Helicobacter pylori infection on gut and intratumoral microbiome and its association with immunotherapy response in gastrointestinal cancer.BMC medicine · 2026Article
- Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems.Frontiers in microbiology · 2026Review
- Metagenomic Data Preprocessing and Quality Control.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.Environmental microbiome · 2025Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.Microbiology spectrum · 2025Article
- Impact of study design, contamination, and data characteristics on results and interpretation of microbiome studies.mSystems · 2025Article
- SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania.Healthcare (Basel, Switzerland) · 2025Article
71 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
10 authors.
Funding
Abstract
Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g., skin swabs, tissue biopsies, ice, water, degraded forensic samples or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over 5 years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a home-made silica-based extraction method, commonly used to analyse low endogenous content samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to modern molecular biology laboratories, and changed over time according to researcher, month and season. The commercial kit also contained higher microbial diversity and several human-associated taxa in comparison to the home-made silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: (a) extraction blank controls should be included and sequenced with every batch of extractions and (b) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.
Indexed as
Identifiers
What OpenQuestion holds
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.