ArticleScientific reports2025
Nanopore full length 16S rRNA gene sequencing increases species resolution in bacterial biomarker discovery.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research.Microbial genomics · 2026Review
- Sentinel plants enable quantitative monitoring of bioavailable nitrate in soils and microbial environments.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Nordic Walking Combined with Time-Restricted Eating Is Associated with Changes in Gut Microbiota Composition in Adults with Obesity-Pilot Study.Nutrients · 2026Article
- Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.Microbial ecology · 2026Article
- Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.Biotech (Basel (Switzerland)) · 2026Article
- Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.Medical mycology · 2026Article
- Effect of sialidase inhibitors on a plaque community biofilm model.Access microbiology · 2026Article
- Plant microbiome engineering: from inoculation to genome editing.Frontiers in microbiology · 2026Review
- Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in thebioRxiv : the preprint server for biology · 2025Article
- Application and Limitations of 16S rRNA Gene Sequencing for Identifying WHO Priority Pathogenic Gram-Negative Bacilli.Infection and drug resistance · 2025Review
- Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.Frontiers in microbiomes · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Discovery of disease-related bacterial biomarkers could be a useful approach for early prevention or diagnosis of various afflictions, such as colorectal cancer. This typically involves analyzing small regions of the 16S rRNA gene (e.g. V3V4) through short-read technologies like Illumina, obtaining genus-level results. However, recent developments in third-generation sequencing, such as Oxford Nanopore Technologies (ONT)'s new R10.4.1 chemistry and its improved basecalling models, are beginning to allow for a more complete and accessible species-level analysis through full-length 16S rRNA gene sequencing (spanning regions V1-V9). Thus, the goal of this study was to compare and evaluate both approaches, using colorectal cancer biomarker discovery as a representative case. This was achieved through the analysis of feces from 123 subjects, comparing both methods (Illumina-V3V4 with DADA2 and QIIME2 vs. ONT-V1V9 with Emu), multiple Dorado basecalling models (fast, hac and sup) and multiple databases (SILVA vs. Emu's Default database). Basecalling models broadly resulted in similar taxonomic output, but had significantly higher observed species and different taxonomic identification the lower the basecalling quality (p-value<0.05). Database choice with Emu influenced the identified species greatly, with Emu's Default database obtaining significantly higher diversity and identified species than SILVA (p-value<0.05). However, it overconfidently classified at times what should be an unknown species as the closest match due to its database structure. Bacterial abundance between Illumina-V3V4 and ONT-V1V9 at the genus level correlated well (R
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