ArticleApplied and environmental microbiology2013
Improved selection of internal transcribed spacer-specific primers enables quantitative, ultra-high-throughput profiling of fungal communities.
Article in Applied and environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 223 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
223 citing papers in PubMed, 1 synthesis or guideline pooled it.
- How quantitative is metabarcoding: A meta-analytical approach.Molecular ecology · 2019Pooled it
- Amplicon Characterization of Fungal Diversity and Functional Prediction of Glycine max L. Rhizosphere Microbiome Under Different Organic Fertilization.MicrobiologyOpen · 2026Article
- An Interpretable Machine Learning Approach to Ecologically Characterize Soil Carbon and Structure From Multi-Kingdom Microbiome, Texture and Climate.Molecular ecology · 2026Article
- Effects of prescribed burning regimes on soil fungal communities, functional traits, and community assembly processes in surface and subsurface peat.FEMS microbiology ecology · 2026Article
- Unraveling yeast diversity in food fermentation using ITS1-2 amplicon-based metabarcoding.Microbiology spectrum · 2026Article
- Dung-Induced Soil Microbial Community Coalescence Driven by Different Dung Sources: Impacts on Community Shifts and Assembly Mechanisms in Grassland Soils.Microorganisms · 2026Article
- Bacterial Diversity and Functional Dynamics in the Soybean (Glycine max L.) Rhizosphere Under Different Organic Fertilisation.Environmental microbiology reports · 2026Article
- Investigating the distribution of antibiotic resistance genes in relation to bacterial, fungal, and functional diversity in a hay field.Microbiology spectrum · 2026Article
- Rapid detection of the plant pathogenic fungi Verticillium longisporum using species-specific fragment and enzyme mediated duplex exponential amplification (EmDEA) assay.World journal of microbiology & biotechnology · 2026Article
- Soil Microbial Diversity in Páramos Wetland of the Colombian Andes Reveals Novel and Unique Features Within a Global Wetland Database.Microbial ecology · 2026Article
- HighALPS: ultra-high-throughput marker-gene amplicon library preparation and sequencing on the Illumina NextSeq and NovaSeq Platforms.mSystems · 2026Article
- Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.Microbiome · 2026Article
- Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems.NPJ biofilms and microbiomes · 2026Article
- Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system.NPJ biofilms and microbiomes · 2026Article
- Prey preference and cell wall-mediated resistance shape predation efficiency in Saccharomycopsis schoenii.FEMS yeast research · 2026Article
- Multi-omic characterization of microbial dynamics during spontaneous fermentation of sweet wine Picolit variety.Frontiers in microbiology · 2026Article
- Spatial heterogeneity and microbial terroir: balancing dispersal limitation and cultivar as drivers of microbial diversity in viticulture.ISME communications · 2026Article
- Impact of winemaking technologies on polyphenolic composition and wine microbiome.Frontiers in microbiology · 2026Article
- Article
- Isolation and identification of dark septate endophytes from sorghum roots and the effects ofFrontiers in microbiology · 2026Article
163 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ultra-high-throughput sequencing (HTS) of fungal communities has been restricted by short read lengths and primer amplification bias, slowing the adoption of newer sequencing technologies to fungal community profiling. To address these issues, we evaluated the performance of several common internal transcribed spacer (ITS) primers and designed a novel primer set and work flow for simultaneous quantification and species-level interrogation of fungal consortia. Primer comparison and validation were predicted in silico and by sequencing a "mock community" of mixed yeast species to explore the challenges of amplicon length and amplification bias for reconstructing defined yeast community structures. The amplicon size and distribution of this primer set are smaller than for all preexisting ITS primer sets, maximizing sequencing coverage of hypervariable ITS domains by very-short-amplicon, high-throughput sequencing platforms. This feature also enables the optional integration of quantitative PCR (qPCR) directly into the HTS preparatory work flow by substituting qPCR with these primers for standard PCR, yielding quantification of individual community members. The complete work flow described here, utilizing any of the qualified primer sets evaluated, can rapidly profile mixed fungal communities and capably reconstructed well-characterized beer and wine fermentation fungal communities.
Indexed as
Identifiers
What OpenQuestion holds
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.