ArticleJCI insight2022
Customization of a DADA2-based pipeline for fungal internal transcribed spacer 1 (ITS1) amplicon data sets.
Article in JCI insight, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 31 citations in OpenAlex.
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- Humanizing Zophobas morio larvae microbiota for rapid screening of emerging decolonization strategies against multidrug-resistant bacteria.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Integrating scanning electron microscopy, explainable deep learning, and ITS sequencing for accurate identification in some species Geastrum.Scientific reports · 2026Article
- Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments.Microorganisms · 2025Article
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- Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.International journal of molecular sciences · 2025Article
- Gut Mycobiome Changes During COVID-19 Disease.Journal of fungi (Basel, Switzerland) · 2025Article
- Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa.Applied and environmental microbiology · 2025Article
- Consequences of "zombie-making" and generalist fungal pathogens on carpenter ant microbiota.Current research in insect science · 2025Article
- The Human Mycobiome.Current topics in microbiology and immunology · 2025Review
- Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.BMC genomics · 2024Article
- Moving beyond species: fungal function in house dust provides novel targets for potential indicators of mold growth in homes.Microbiome · 2024Article
- How do high phosphate concentrations affect soil microbial communities after a century of ecosystem self-reclamation?Environmental microbiology reports · 2024Article
- Refermentation and maturation of lambic beer in bottles: a necessary step for gueuze production.Applied and environmental microbiology · 2024Article
- Enhancing ascitic fungal infection diagnosis through next-generation sequencing: a pilot study in surgical ICU patients.Frontiers in cellular and infection microbiology · 2024Article
- The airway mycobiome and interactions with immunity in health and chronic lung disease.Oxford open immunology · 2024Review
- Bacterial, but not fungal, communities show spatial heterogeneity in European beech (Fagus sylvatica L.) deadwood.FEMS microbiology ecology · 2023Article
- Profiling the Fungal Microbiome after Fecal Microbiota Transplantation for Graft-versus-Host Disease: Insights from a Phase 1 Interventional Study.Transplantation and cellular therapy · 2023Article
- Review
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Identification and analysis of fungal communities commonly rely on internal transcribed spacer-based (ITS-based) amplicon sequencing. There is no gold standard used to infer and classify fungal constituents since methodologies have been adapted from analyses of bacterial communities. To achieve high-resolution inference of fungal constituents, we customized a DADA2-based pipeline using a mix of 11 medically relevant fungi. While DADA2 allowed the discrimination of ITS1 sequences differing by single nucleotides, quality filtering, sequencing bias, and database selection were identified as key variables determining the accuracy of sample inference. Due to species-specific differences in sequencing quality, default filtering settings removed most reads that originated from Aspergillus species, Saccharomyces cerevisiae, and Candida glabrata. By fine-tuning the quality filtering process, we achieved an improved representation of the fungal communities. By adapting a wobble nucleotide in the ITS1 forward primer region, we further increased the yield of S. cerevisiae and C. glabrata sequences. Finally, we showed that a BLAST-based algorithm based on the UNITE+INSD or the NCBI NT database achieved a higher reliability in species-level taxonomic annotation compared with the naive Bayesian classifier implemented in DADA2. These steps optimized a robust fungal ITS1 sequencing pipeline that, in most instances, enabled species-level assignment of community members.
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Registered trials
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