ArticleScientific reports2020
Evaluation of PCR conditions for characterizing bacterial communities with full-length 16S rRNA genes using a portable nanopore sequencer.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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.
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Who cites it
25 citing papers in PubMed, 64 citations in OpenAlex.
- Full-Length 16S rRNA Amplicon Sequencing for the Simple and Simultaneous Detection of Multiple Probiotic Species in Commercial Products.Journal of microbiology and biotechnology · 2026Article
- Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.Microorganisms · 2026Review
- Comparison of Lysis and Amplification Methodologies for Optimal 16S rRNA Gene Profiling for Human and Mouse Microbiome Studies.International journal of molecular sciences · 2025Article
- Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.Frontiers in microbiology · 2025Article
- From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases.Diagnostics (Basel, Switzerland) · 2024Review
- Differential characteristics of vaginal versus endometrial microbiota in IVF patients.Scientific reports · 2024Article
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
- A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.Archives of microbiology · 2024Article
- Identification and florfenicol-treatment of pseudomonas putida infection in gilthead seabream (Sparus aurata) fed on tilapia-trash-feed.BMC veterinary research · 2024Article
- Comparison of nine extraction methods for bacterial identification using the ONT MinION sequencer.International journal of legal medicine · 2024Article
- Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil.Scientific reports · 2023Article
- SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.ISME communications · 2023Article
- Article
- Atlantic Salmon (Microorganisms · 2022Article
- Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma.Microbiology spectrum · 2022Article
- Metaprofiling of the Bacterial Community in Colonized Compost Extracts byJournal of fungi (Basel, Switzerland) · 2022Article
- Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data.Nature methods · 2022Article
- Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study.Brain, behavior, & immunity - health · 2022Article
- A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data.Microorganisms · 2022Article
- Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MinION (Oxford Nanopore Technologies), a portable nanopore sequencer, was introduced in 2014 as a new DNA sequencing technology. MinION is now widely used because of its low initial start-up costs relative to existing DNA sequencers, good portability, easy-handling, real-time analysis and long-read output. However, differences in the experimental conditions used for 16S rRNA-based PCR can bias bacterial community assessments in samples. Therefore, basic knowledge about reliable experimental conditions is needed to ensure the appropriate use of this technology. Our study concerns the reliability of techniques for obtaining accurate and quantitative full-length 16S rRNA amplicon sequencing data for bacterial community structure assessment using MinION. We compared five PCR conditions using three independent mock microbial community standard DNAs and established appropriate, standardized, better PCR conditions among the trials. We then sequenced two mock communities and six environmental samples using Illumina MiSeq for comparison. Modifying the PCR conditions improved the sequencing quality; the optimized conditions were 35 cycles of 95 °C for 1 min, 60 °C for 1 min and 68 °C for 3 min. Our results provide important information for researchers to determine bacterial community using MinION accurately.
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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.