ArticleInternational journal of molecular sciences2019
TARGETING THE 16S RRNA GENE FOR BACTERIAL IDENTIFICATION IN COMPLEX MIXED SAMPLES: COMPARATIVE EVALUATION OF SECOND (ILLUMINA) AND THIRD (OXFORD NANOPORE TECHNOLOGIES) GENERATION SEQUENCING TECHNOLOGIES.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- Performance and practicality of 16S nanopore sequencing for routine bacterial identification in clinical samples.Microbiology spectrum · 2026Article
- Analytic attributes of the 16S rRNA gene sequencing methodology for human gut microbiota characterization.Applied microbiology and biotechnology · 2026Article
- Exploring the oral microbiome: from traditional techniques to advanced omics and databases.Antonie van Leeuwenhoek · 2026Review
- Oral and plasma microbiome in the context of acute febrile illness.medRxiv : the preprint server for health sciences · 2026Article
- The Potential of Bioinformatics in Revolutionizing Disease Diagnosis in Sub-Saharan Africa: A Narrative Review.Health science reports · 2026Article
- Potential use of whey in kefir production: evaluation of fermentation kinetics and microbiota.Food science of animal resources · 2026Article
- Hidden Partners in Diversity: Acidobacteriota and Their Distribution in the Cape Floristic Region.MicrobiologyOpen · 2026Article
- Cross-Platform Evaluation of Established NGS-Based Metabarcoding Methods for Detecting Food Fraud in Pistachio Products.Foods (Basel, Switzerland) · 2026Article
- Diagnostic challenges in postoperative pelvic infections associated withFrontiers in cellular and infection microbiology · 2026Article
- The prevalence and distribution ofFrontiers in microbiomes · 2026Article
- Microbial dysbiosis and inferred functional profiling reveals the potential role ofFrontiers in cellular and infection microbiology · 2026Article
- Ecological origin and naturalCurrent research in parasitology & vector-borne diseases · 2026Article
- An interdisciplinary scoping review of the emerging impact of periocular skincare products on the ocular surface microbiome and tear film stability.Frontiers in cellular and infection microbiology · 2026Article
- Antibiotic Resistance Crisis: From Bacterial Bioprospecting to Artificial Intelligence.Environmental microbiology reports · 2025Review
- A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.Molecular ecology resources · 2025Article
- Evaluation of biofilm formation, antimicrobial pattern, and typing of Stenotrophomonas maltophilia isolated from clinical sources in Brazil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Evaluation of V3-V4 and FL-16S rRNA amplicon sequencing approach for microbiota community analysis of tracheostomy aspirates.mSphere · 2025Article
- The Impact of Bariatric Surgery on Gut Microbiota Composition and Diversity: A Longitudinal Analysis Using 16S rRNA Sequencing.International journal of molecular sciences · 2025Article
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- Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.Journal of assisted reproduction and genetics · 2025Article
44 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
Abstract
Rapid, accurate bacterial identification in biological samples is an important task for microbiology laboratories, for which 16S~rRNA gene Sanger sequencing of cultured isolates is frequently used. In contrast, next-generation sequencing does not require intermediate culturing steps and can be directly applied on communities, but its performance has not been extensively evaluated. We present a comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies (ONT)) generation sequencing technologies for 16S targeted genomics using a well-characterized reference sample. Different 16S gene regions were amplified and sequenced using the Illumina MiSeq, and analyzed with Mothur. Correct classification was variable, depending on the region amplified. Using a majority vote over all regions, most false positives could be eliminated at the genus level but not the species level. Alternatively, the entire 16S gene was amplified and sequenced using the ONT MinION, and analyzed with Mothur, EPI2ME, and GraphMap. Although >99\% of reads were correctly classified at the genus level, up to $\approx$40\% were misclassified at the species level. Both~technologies, therefore, allow reliable identification of bacterial genera, but can potentially misguide identification of bacterial species, and constitute viable alternatives to Sanger sequencing for rapid analysis of mixed samples without requiring any culturing steps.
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