ArticleFrontiers in cellular and infection microbiology2022
Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing.
Article in Frontiers in cellular and infection microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 25 citations in OpenAlex.
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.Microbial genomics · 2026Article
- Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.Microbiome · 2026Article
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Microbial community characterization in Red Sea-derived samples using a field-deployable DNA extraction system and nanopore sequencing.Environmental microbiome · 2025Article
- Rapid Nanopore Sequencing of Positive Blood Cultures Using Automated Benzyl-Alcohol Extraction Improves Time-Critical Sepsis Management.Antibiotics (Basel, Switzerland) · 2025Article
- Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases.Journal of epidemiology and global health · 2025Review
- The Symbiotic Bacterial Profile of Laboratory-Reared and Field-CaughtMicroorganisms · 2025Article
- Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.Scientific reports · 2024Article
- Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Evaluation of Commercial RNA Extraction Protocols for Avian Influenza Virus Using Nanopore Metagenomic Sequencing.Viruses · 2024Article
- Impact of cell lysis treatment before saliva metagenomic DNA extraction on the oral microbiome and the associated resistome.Clinical and experimental dental research · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.Access microbiology · 2024Article
- Review
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic next-generation sequencing (mNGS) is a novel useful strategy that is increasingly used for pathogens detection in clinic. Some emerging mNGS technologies with long-read ability are useful to decrease sequencing time and increase diagnosed accuracy, which is of great significance in rapid pathogen diagnosis. Reliable DNA extraction is considered critical for the success of sequencing; hence, there is thus an urgent need of gentle DNA extraction method to get unbiased and more integrate DNA from all kinds of pathogens. In this study, we systematically compared three DNA extraction methods (enzymatic cell lysis based on MetaPolyzyme, mechanical cell lysis based on bead beating, and the control method without pre-cell lysis, respectively) by assessing DNA yield, integrity, and the microbial diversity based on long-read nanopore sequencing of urine samples with microbial infections. Compared with the control method, the enzymatic-based method increased the average length of microbial reads by a median of 2.1-fold [Inter Quartile Range (IQR), 1.7-2.5; maximum, 4.8) in 18 of the 20 samples and the mapped reads proportion of specific species by a median of 11.8-fold (Inter Quartile Range (IQR), 6.9-32.2; maximum, 79.27]. Moreover, it provided fully (20 of 20) consistent diagnosed results to the clinical culture and more representative microbial profiles (
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Registered trials
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