ArticleMicrobiome2023
Using strain-resolved analysis to identify contamination in metagenomics data.
Article in Microbiome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.Microbial genomics · 2026Article
- Mother-to-offspring microbial vertical transmission: timing, determinants, and impact on offspring susceptibility to gastrointestinal diseases.Medical review (2021) · 2026Review
- CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.Nature communications · 2026Article
- Comparative study of the physicochemical properties, volatile compounds, and bacterial microbiota in commercial and traditional yak yogurt from the Qinghai-Tibet plateau.Food chemistry: X · 2026Article
- Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.The Journal of infectious diseases · 2026Review
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.Frontiers in microbiology · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial genomics · 2026Article
- Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- Negativeome characterization and decontamination in early-life virome studies.Nature communications · 2025Article
- Guidelines for preventing and reporting contamination in low-biomass microbiome studies.Nature microbiology · 2025Review
- Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.ACS ES&T engineering · 2025Article
- Article
- Photodynamic Therapy with Protoporphyrin IX Precursors Using Artificial Daylight Improves Skin Antisepsis for Orthopedic Surgeries.Microorganisms · 2025Article
- Tracking the origin of bacterial DNA in blood: Indication of localized and sporadic transfer from other body sites.Gut microbes reports · 2025Article
- Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.Microorganisms · 2024Review
- A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa.BMC genomics · 2024Article
- Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems.NPJ biofilms and microbiomes · 2024Article
- Infant gut DNA bacteriophage strain persistence during the first 3 years of life.Cell host & microbe · 2024Article
- Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.Nature biotechnology · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundMetagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.
resultsHere, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass.
conclusionOur work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.
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