ArticleScientific reports2023
Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Acute fungal post-cataract endophthalmitis in the endophthalmitis management study: EMS report 7.BMJ open ophthalmology · 2025Trial
- Phytochemical Profiling and Evaluation of Antibacterial, Anticancer, Anti-inflammatory, and Wound-Healing Activities of Endophytic Fungi Isolated From Atalantia racemosa.Chemistry & biodiversity · 2026Article
- Comparative evaluation of conventional and nanopore approaches in onychomycosis diagnosis.Diagnostic microbiology and infectious disease · 2026Article
- Biocontrol Microbial Inoculants SuppressPlants (Basel, Switzerland) · 2026Article
- Microbiome legacy influences necrosis formation in Diplodia sapinea-infected Scots pine shoots.Environmental microbiome · 2026Article
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- MMonitor for real-time monitoring of microbial communities using long reads.Cell reports methods · 2026Article
- DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.Antonie van Leeuwenhoek · 2026Review
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- Targeted long-read sequencing analysis and antifungal susceptibility profiles of Sporothrix schenckii isolates from Thailand.PLoS neglected tropical diseases · 2025Article
- Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota.Environmental microbiome · 2025Article
- Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.International journal of molecular sciences · 2025Article
- Impact of Fermentation on Bacterial and Fungal Microbiome Interactions inInternational journal of food science · 2025Article
- Improving the profiling of wheat bacterial and fungal endophytic communities-a PCR clamping approach.Frontiers in microbiology · 2025Article
- Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?Expert review of molecular diagnostics · 2024Review
- The Effects of Brodalumab on the Fungal Microbiome in Patients with Psoriasis.International journal of molecular sciences · 2024Article
- EnsembleSeq: a workflow towards real-time, rapid, and simultaneous multi-kingdom-amplicon sequencing for holistic and resource-effective microbiome research at scale.Microbiology spectrum · 2024Article
- Predictive phage therapy forProceedings of the National Academy of Sciences of the United States of America · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The study of microbiota has been revolutionized by the development of DNA metabarcoding. This sequence-based approach enables the direct detection of microorganisms without the need for culture and isolation, which significantly reduces analysis time and offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there has been an accumulating number of researches on bacteria, molecular phylogenetic analysis of fungi still remains challenging due to the lack of standardized tools and the incompleteness of reference databases limiting the accurate and precise identification of fungal taxa. Here, we present a DNA metabarcoding workflow for characterizing fungal microbiota with high taxonomic resolution. This method involves amplifying longer stretches of ribosomal RNA operons and sequencing them using nanopore long-read sequencing technology. The resulting reads were error-polished to generate consensus sequences with 99.5-100% accuracy, which were then aligned against reference genome assemblies. The efficacy of this method was explored using a polymicrobial mock community and patient-derived specimens, demonstrating the marked potential of long-read sequencing combined with consensus calling for accurate taxonomic classification. Our approach offers a powerful tool for the rapid identification of pathogenic fungi and has the promise to significantly improve our understanding of the role of fungi in health and disease.
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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.