Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota
Illumina and Oxford Nanopore Technologies metabarcoding captured similar host-dependent diversity patterns despite observed differences in numbers and composition of fungi. Short-read metabarcoding might be optimal for fungal biodiversity studies due to higher sequencing depths and resultant breadth of diversity. As error rates are continuing to decrease, reference databases expand, and throughput improves, long-read metabarcoding is becoming a strong candidate for future diagnostic studies of fungi. Traditional culturing captures most of the fungi from short-read metabarcoding and remains valuable for obtaining isolates for further research.
Authors
- Quirin Kupper (ORCID: https://orcid.org/0009-0007-4325-822X)
- René Eschen (ORCID: https://orcid.org/0000-0002-0464-6680)
- Renate Heinzelmann (ORCID: https://orcid.org/0009-0004-4599-8430)
- Martin Hartmann (ORCID: https://orcid.org/0000-0001-8069-5284)
- Salome Schneider (ORCID: https://orcid.org/0000-0003-2235-964X)
- Simone Prospero (ORCID: https://orcid.org/0000-0002-9129-8556)
- Iva Franić (ORCID: https://orcid.org/0000-0002-3352-0956)
- Jana Mittelstrass (ORCID: https://orcid.org/0000-0001-5207-5520)
Institutions
- Swiss Federal Institute for Forest, Snow and Landscape Research (CH)
- ETH Zurich (CH)
- CABI Switzerland (CH)
Publication Details
- Journal
- Environmental Microbiome
- Published
- 2025-05-19
- DOI
- https://doi.org/10.1186/s40793-025-00712-7
- Citations
- 5
- Primary Topic
- Plant Pathogens and Fungal Diseases
- Type
- article
- Field-Weighted Citation Impact
- 5.76
Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Eidgenössische Technische Hochschule Zürich