ArticleBiology methods & protocols2021
Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples.
Article in Biology methods & protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 65 citations in OpenAlex.
- Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding.Microbiology spectrum · 2026Article
- Comparative evaluation of conventional and nanopore approaches in onychomycosis diagnosis.Diagnostic microbiology and infectious disease · 2026Article
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- High-Resolution Community Profiling of Active Bacteria and Eukaryotes in Replant-Diseased Blueberry Farm Soils From New Jersey, USA.Environmental microbiology · 2026Article
- A discriminative primer design workflow enables selective metabarcoding, demonstrated using long-read sequencing of endophytic fungi.FEMS microbiology ecology · 2026Article
- Molecular Identification and RNA-Based Management of Fungal Plant Pathogens: From PCR to CRISPR/Cas9.International journal of molecular sciences · 2026Review
- Article
- Nanopore 16S-Full Length and ITS Sequencing for Microbiota Identification in Intra-Abdominal Infections.Diagnostics (Basel, Switzerland) · 2025Article
- Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis?Microorganisms · 2025Review
- MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers.Microbial genomics · 2025Article
- Advanced rDNA-Based Detection of Wheat Pathogens in Grain Samples Using Next-Generation Sequencing (NGS).Pathogens (Basel, Switzerland) · 2025Article
- Improving the profiling of wheat bacterial and fungal endophytic communities-a PCR clamping approach.Frontiers in microbiology · 2025Article
- Detection of fungal sequences in human brain: rDNA locus amplification and deep sequencing.Scientific reports · 2024Article
- Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data.Briefings in bioinformatics · 2024Article
- Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease.Biomedical reports · 2024Article
- Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations.Environmental microbiome · 2024Article
- Fecal Mycobiota in Patients with Inflammatory Bowel Diseases and Extraintestinal Manifestations.Gut microbes reports · 2024Article
- Diabetes and gut microbiome.Frontiers in microbiology · 2024Review
- Long amplicon nanopore sequencing ofBiology methods & protocols · 2024Article
- Genetic diversity and population differentiation in Earliella scabrosa, a pantropical species of Polyporales.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level and in real-time. We assess the applicability for taxonomic assignment of amplicons targeting a 3.5 Kb region (V3 18S-ITS1-5.8S-ITS2-28S D2) and a 6 Kb region (V1 18S-ITS1-5.8S-ITS2-28S D12) with the What's in my pot (WIMP) classifier. We used the ZymoBIOMICS
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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.