ArticleNature communications2022
A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- Review
- Refining the Clinical Utility of Plasma Microbial Cell-Free DNA Sequencing in High-Risk Population of Infection: A Narrative Review.Infection and drug resistance · 2026Review
- A peritoneal effluent sequencing assay that removes environmental DNA contamination in peritoneal dialysis patients.Clinical kidney journal · 2026Article
- Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis.Research square · 2025Article
- A metagenomic approach for microbial risk assessment and source attribution in high-risk ports of entry environments.Biosafety and health · 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
- Advancements and Prospects in DNA-Based Bioanalytical Technology for Environmental Toxicant Detection.JACS Au · 2025Review
- The environmental microbial retrieving assessment of cell-processing facilities for cell therapy in a hospital laboratory.Microbiology spectrum · 2024Article
- Plasma cell-free RNA signatures of inflammatory syndromes in children.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers.Scientific reports · 2024Article
- A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections.Microbiology spectrum · 2024Article
- Gut-liver axis: barriers and functional circuits.Nature reviews. Gastroenterology & hepatology · 2023Review
- Revealing influencing factors on global waste distribution via deep-learning based dumpsite detection from satellite imagery.Nature communications · 2023Article
- Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnostic of Fungal Pathogens in Plants.Journal of fungi (Basel, Switzerland) · 2022Review
- Pathogen Detection by Metagenomic Next-Generation Sequencing During Neutropenic Fever in Patients With Hematological Malignancies.Open forum infectious diseases · 2022Article
- A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.Nature communications · 2022Article
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
Abstract
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) a metagenomic sequencing assay that is robust against environmental DNA contamination introduced during sample preparation. The core idea of SIFT-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied SIFT-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of sepsis and inflammatory bowel disease in blood.
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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.