ArticleBMC genomics2023
Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 50 citations in OpenAlex.
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- Unveiling hidden microbial diversity in Mars 2020 mission assembly cleanrooms with molecular insights into the persistence and perseverance of novel species defying metagenome sequencing.Microbiology spectrum · 2026Article
- Cave microbial communities are structured by environmental matrix and depth and can be characterized with field-portable assays.Applied and environmental microbiology · 2026Article
- A Simplified and Efficient Protocol for DNA Isolation from Deer Antlers and Prepared Trophy Skulls.Animals : an open access journal from MDPI · 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
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- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- Development and optimization of host DNA depletion in blood cultures using a saponin and salt-activated nuclease-based method.Frontiers in microbiology · 2026Article
- Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.Microbiome · 2025Article
- Sample Preparation for Multi-Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow.Proteomics · 2025Review
- Article
- Rapid Nanopore Sequencing of Positive Blood Cultures Using Automated Benzyl-Alcohol Extraction Improves Time-Critical Sepsis Management.Antibiotics (Basel, Switzerland) · 2025Article
- Optimization of DNA extraction methods from pig farm wastewater for pathogen detection using metagenomic sequencing.Microbial genomics · 2025Article
- Design, Development, and Clinical Validation of a Novel Kit for Cell-Free DNA Extraction.Diagnostics (Basel, Switzerland) · 2025Article
- Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis.BMC genomics · 2025Article
- Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- The gut microbiome and cancer: from tumorigenesis to therapy.Nature metabolism · 2025Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and helps to resolve complex genomic contexts, especially in the case of metagenome analysis. To take the best advantage of long-read sequencing, DNA extraction methods must be able to isolate pure high molecular weight (HMW) DNA from complex metagenomics samples, without introducing any bias. New methods released on the market, and protocols developed at the research level, were specifically designed for this application and need to be assessed.
resultsIn this study, with different bacterial cocktail mixes, analyzed as pure or spiked in a synthetic fecal matrix, we evaluated the performances of 6 DNA extraction methods using various cells lysis and purification techniques, from quick and easy, to more time-consuming and gentle protocols, including a portable method for on-site application. In addition to the comparison of the quality, quantity and purity of the extracted DNA, the performance obtained when doing Nanopore sequencing on a MinION flow cell was also tested. From the obtained results, the Quick-DNA HMW MagBead Kit (Zymo Research) was selected as producing the best yield of pure HMW DNA. Furthermore, this kit allowed an accurate detection, by Nanopore sequencing, of almost all the bacterial species present in a complex mock community.
conclusionAmongst the 6 tested methods, the Quick-DNA HMW MagBead Kit (Zymo Research) was considered as the most suitable for Nanopore sequencing and would be recommended for bacterial metagenomics studies using this technology.
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