ArticleCell reports2019
Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles.
Article in Cell reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers, 1 of them a synthesis that pooled it.
What it found
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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
109 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives.Drugs · 2021Pooled it
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.Microbiology spectrum · 2026Article
- Optimized Urine Metagenomic Methods Reveal Longitudinal Microbial Community Dynamics and Predictors of Transition from Asymptomatic Colonization to CAUTI.bioRxiv : the preprint server for biology · 2026Article
- Optimisation and validation of capture mNGS for predicting antimicrobial resistance.EBioMedicine · 2026Article
- Viral Detection and Clinical Disease Features in Pediatric Chronic Rhinosinusitis.Laryngoscope investigative otolaryngology · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.Biology · 2026Review
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Respiratory viral infection is associated with increasedERJ open research · 2026Article
- Antibiotic-induced gut microbiome remodeling reduces neuroinflammation in traumatic brain injury.Communications biology · 2026Article
- Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.Microbiology spectrum · 2026Article
- Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.medRxiv : the preprint server for health sciences · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Metagenomics next-generation sequencing of plasma combined with blood cells for improving the prognosis of early infection in patients with hematologic disorders: a real-world cohort study in northern China.Frontiers in molecular biosciences · 2026Article
- Review
- Clinical utility of metagenomic next-generation sequencing (mNGS) and a novel PCR-based point-of-care testing (POCT) for pathogen detection in pulmonary infections: a retrospective study.BMC infectious diseases · 2025Article
- CFTR modulator therapy drives microbiome restructuring through improved host physiology in cystic fibrosis: the IMMProveCF phase IV trial.Nature communications · 2025Article
- Assessing the Oral Microbiome in Women of Reproductive Age: A Narrative Review.Clinics and practice · 2025Review
49 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens.
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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.