ArticleBMC microbiology2018
A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms.
Article in BMC microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Accurate monitoring of substrate-dependent growth reveals ecotypic differentiation among marine yeasts.ISME communications · 2026Article
- Cross-country multi-modal evidence links Aspergillus to biliary atresia.Gut pathogens · 2025Article
- Beyond dikarya: 28S metabarcoding uncovers cryptic fungal lineages across a tidal estuary.Environmental microbiome · 2025Article
- Environmental Yeast Abundance and Diversity Assessment in Recreation Areas of Bangkok, Thailand.Environmental microbiology reports · 2025Article
- Identifying the drivers of microbial community changes and interactions in polluted coastal sediments.Environmental microbiome · 2025Article
- Compartment-specific microbial communities highlight the ecological roles of fungi in a subtropical seagrass ecosystem.Applied and environmental microbiology · 2025Article
- Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq).bioRxiv : the preprint server for biology · 2025Article
- Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host.The ISME journal · 2025Article
- Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling.Frontiers in bioinformatics · 2025Article
- Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.ISME communications · 2025Article
- Next-generation sequencing applications in food science: fundamentals and recent advances.Frontiers in bioengineering and biotechnology · 2025Review
- Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Cast from the Past? Microbial Diversity of a Neolithic Stone Circle.Microorganisms · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups.
resultsWe performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides.
conclusionsThe compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.
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