ArticleInternational journal of molecular sciences2019
Optimisation and Benchmarking of Targeted Amplicon Sequencing for Mycobiome Analysis of Respiratory Specimens.
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 20 papers.
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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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Who cites it
20 citing papers in PubMed.
- Stress-induced toxic genomic R-loops support biofilm extracellular matrix formation.Nature communications · 2025Article
- The human mycobiome: a critical yet understudied component of health and disease.Microbiology (Reading, England) · 2025Review
- The fungal microbiota modulate neonatal oxygen-induced lung injury.Microbiome · 2025Article
- Impact of diet on the gut mycobiome of Hong Kong Chinese infants.Computational and structural biotechnology journal · 2025Article
- Infection and the microbiome in bronchiectasis.European respiratory review : an official journal of the European Respiratory Society · 2024Review
- Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome.Microbiome research reports · 2024Review
- RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms.Nature communications · 2023Article
- Respiratory microbiota and radiomics features in the stable COPD patients.Respiratory research · 2023Article
- The Skin Microbiome: Current Techniques, Challenges, and Future Directions.Microorganisms · 2023Review
- Applying Next-Generation Sequencing and Multi-Omics in Chronic Obstructive Pulmonary Disease.International journal of molecular sciences · 2023Review
- The Human Mycobiome: Colonization, Composition and the Role in Health and Disease.Journal of fungi (Basel, Switzerland) · 2022Review
- ClinicalJournal of fungi (Basel, Switzerland) · 2022Review
- The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives.Microorganisms · 2022Review
- Mycobiome in the Middle Ear Cavity with and Without Otitis Media with Effusion.Turkish archives of otorhinolaryngology · 2021Article
- Respiratory Mycoses in COPD and Bronchiectasis.Mycopathologia · 2021Review
- Inhaled Corticosteroids and the Lung Microbiome in COPD.Biomedicines · 2021Review
- Integrative microbiomics in bronchiectasis exacerbations.Nature medicine · 2021Article
- Evaluation of Droplet Digital Polymerase Chain Reaction (ddPCR) for the Absolute Quantification ofInternational journal of molecular sciences · 2020Article
- The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges.Mycopathologia · 2020Review
- Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter?PloS one · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
(1) Background: Firm consensus has yet to be established in relation to taxonomic classification and primer choice in targeted amplicon sequencing of the mycobiome. While the nuclear ribosomal internal transcribed spacer (ITS) region are recognized as the formal fungal taxonomic barcode, appraisal of different ITS sub-regions and the influence of DNA extraction methods have not been comprehensively undertaken using human respiratory specimens. (2) Methods: We performed ITS analysis of respiratory (sputum) samples by assessing (a) the effect of alternate DNA extraction techniques and (b) an evaluation of four different ITS primer pairs (ITS1F and ITS2; ITS1-30F and ITS1-217R; gITS7ngs and ITS4ng; and Fseq and Rseq) on the mycobiome profiles generated for mock fungal communities and their respective clinical (airway) specimens. (3) Results: Primer pairs varied in their resulting ITS mycobiome profiles, suggesting that particular pairs may be more relevant for analysis of respiratory samples compared to others. Assessment of DNA extraction methods highlighted lower final DNA concentrations achieved by mechanical disruption compared to enzymatic lysis. However, despite lower yields, DNA liberated by mechanical lysis more readily yielded ITS bands with highest success in combination with the Fseq and Rseq primers. (4) Conclusion: Choice of extraction method, primers used, and sequencing approach are all important considerations in sequencing the mycobiome and should be tailored to sample type. A standardization of approach to mycobiome studies using respiratory specimens will permit more reliable comparisons between studies and improve our understanding of the role of fungi in the human airway.
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