ArticleFEBS open bio2019
Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer.
Article in FEBS open bio, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Isolation and characterization of Shouchella clausii MJ1G0B, a novel halotolerant bacterium from Madura salt ponds: a putative Valenciaxanthin-like xanthophyll with antioxidant and antibacterial activities.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- A Simple, Rapid and Reliable Protocol for Extraction of High Quality Bacterial Genomic DNA Directly from Potato Tubers for Efficient PCR-Based Surveillance and Molecular Characterization ofMethods and protocols · 2026Article
- Quality control strategy for differentiating induced pluripotent stem cells into pancreatic β-cells before transplantation.Regenerative medicine · 2026Review
- The Antimicrobial and Cytotoxic Activity of Green-Synthesized Silver Nanoparticle Extract of Marine Bacteria and Their 16S rRNA Identification and Characterization.Bioinorganic chemistry and applications · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Advances in methods for rapid detection of Staphylococcus aureus and methicillin-resistant S. aureus.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2025Review
- Nematicidal and plant growth-promoting rhizobacteria: a sustainable strategy for controlling Tylenchulus semipenetrans and enhancing citrus growth.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- Comparison of Lysis and Amplification Methodologies for Optimal 16S rRNA Gene Profiling for Human and Mouse Microbiome Studies.International journal of molecular sciences · 2025Article
- Formulation and Quality Assessment of a FunctionalInternational journal of food science · 2025Article
- Multi-platform metagenomic characterization of the microbial community during spontaneous cacao fermentation.Frontiers in bioengineering and biotechnology · 2025Article
- Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes.International journal of molecular sciences · 2024Article
- Rapid bacterial identification through volatile organic compound analysis and deep learning.BMC bioinformatics · 2024Article
- Nodulation Experiment by Cross-Inoculation of Nitrogen-Fixing Bacteria Isolated from Root Nodules of Several Leguminous Plants.Journal of microbiology and biotechnology · 2024Article
- Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.BMC medical genomics · 2024Article
- Advancement of Carotenogenesis of Astaxanthin from Haematococcus pluvialis: Recent Insight and Way Forward.Molecular biotechnology · 2024Review
- Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer.International journal of legal medicine · 2024Article
- The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.Applied and environmental microbiology · 2023Article
- Critical evaluation of strategies to achieve direct real-time PCR detection of swine pathogens in oral fluids.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2023Article
- The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis.International ophthalmology · 2023Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid identification of bacterial pathogens is crucial for appropriate and adequate antibiotic treatment, which significantly improves patient outcomes. 16S ribosomal RNA (rRNA) gene amplicon sequencing has proven to be a powerful strategy for diagnosing bacterial infections. We have recently established a sequencing method and bioinformatics pipeline for 16S rRNA gene analysis utilizing the Oxford Nanopore Technologies MinION™ sequencer. In combination with our taxonomy annotation analysis pipeline, the system enabled the molecular detection of bacterial DNA in a reasonable time frame for diagnostic purposes. However, purification of bacterial DNA from specimens remains a rate-limiting step in the workflow. To further accelerate the process of sample preparation, we adopted a direct PCR strategy that amplifies 16S rRNA genes from bacterial cell suspensions without DNA purification. Our results indicate that differences in cell wall morphology significantly affect direct PCR efficiency and sequencing data. Notably, mechanical cell disruption preceding direct PCR was indispensable for obtaining an accurate representation of the specimen bacterial composition. Furthermore, 16S rRNA gene analysis of mock polymicrobial samples indicated that primer sequence optimization is required to avoid preferential detection of particular taxa and to cover a broad range of bacterial species. This study establishes a relatively simple workflow for rapid bacterial identification via MinION™ sequencing, which reduces the turnaround time from sample to result, and provides a reliable method that may be applicable to clinical settings.
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