ArticleApplied and environmental microbiology2023
The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.
Article in Applied and environmental microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07381140 (Longitudinal Evaluation of Gut Microbiota and Fecal Metabolome Following Roux-en-Y Gastric Bypass), which is not on this map. Cited by 109 papers, 1 of them a synthesis that pooled it.
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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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Longitudinal Evaluation of Gut Microbiota and Fecal Metabolome Following Roux-en-Y Gastric Bypass: Clinical Implications and Identification of Predictive Biomarkers
Who cites it
109 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic Review: Long-Read Sequencing in Algal Studies.International journal of molecular sciences · 2026Pooled it
- Gut Microbiome Diversity, Functional Potential, and Ecological Relevance of Hottentotta tamulus.MicrobiologyOpen · 2026Article
- Re-Emerging Bacterial Pathogens, Resistance Genes and Promising Bioindicators in Raw and Treated Sewage-Addressing a Known Issue from a Different Angle and Perspective.Microorganisms · 2026Article
- Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics.PLoS neglected tropical diseases · 2026Article
- Sea Lice (Lepeophtheirus salmonis) Harbour Putative Fish Pathogens: Insights From Illumina and Nanopore Sequencing.Journal of fish diseases · 2026Article
- A scalable and cost-effective nanopore workflow for 16S rRNA microbiome profiling validated in a zebrafish gut model.Microbial genomics · 2026Article
- Topographic decoupling of tree-mortality disturbances drives contrasting soil carbon fates via divergent microbial strategies.Nature communications · 2026Article
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Article
- A Multilocus Nanopore eDNA Workflow for Red Algal Diversity Assessment in an Algal Reef System.Ecology and evolution · 2026Article
- rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.Yeast (Chichester, England) · 2026Article
- Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing.Journal of medical microbiology · 2026Article
- Article
- A microbial consortium constructed with gut microbes of Chinese native chicken breeds protects chicks against Salmonella infection.Journal of animal science and biotechnology · 2026Article
- Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing.Microbial genomics · 2026Article
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- Article
- 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
- DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.Molecular ecology resources · 2026Article
- Oral and plasma microbiome in the context of acute febrile illness.medRxiv : the preprint server for health sciences · 2026Article
49 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
The long-read amplicon provides a species-level solution for the community. With the improvement of nanopore flowcells, the accuracy of Oxford Nanopore Technologies (ONT) R10.4.1 has been substantially enhanced, with an average of approximately 99%. To evaluate its effectiveness on amplicons, three types of microbiomes were analyzed by 16S ribosomal RNA (hereinafter referred to as "16S") amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1) in the current study. We showed the error rate, recall, precision, and bias index in the mock sample. The error rate of ONT R10.4.1 was greatly reduced, with a better recall in the case of the synthetic community. Meanwhile, in different types of environmental samples, ONT R10.4.1 analysis resulted in a composition similar to Pacbio data. We found that classification tools and databases influence ONT data. Based on these results, we conclude that the ONT R10.4.1 16S amplicon can also be used for application in environmental samples. IMPORTANCE The long-read amplicon supplies the community with a species-level solution. Due to the high error rate of nanopore sequencing early on, it has not been frequently used in 16S studies. Oxford Nanopore Technologies (ONT) introduced the R10.4.1 flowcell with Q20+ reagent to achieve more than 99% accuracy as sequencing technology advanced. However, there has been no published study on the performance of commercial PromethION sequencers with R10.4.1 flowcells on 16S sequencing or on the impact of accuracy improvement on taxonomy (R9.4.1 to R10.4.1) using 16S ONT data. In this study, three types of microbiomes were investigated by 16S ribosomal RNA (rRNA) amplicon sequencing using Novaseq, Pacbio sequel II, and Nanopore PromethION platforms (R9.4.1 and R10.4.1). In the mock sample, we displayed the error rate, recall, precision, and bias index. We observed that the error rate in ONT R10.4.1 is significantly lower, especially when deletions are involved. First and foremost, R10.4.1 and Pacific Bioscience platforms reveal a similar microbiome in environmental samples. This study shows that the R10.4.1 full-length 16S rRNA sequences allow for species identification of environmental microbiota.
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