ReviewThe New phytologist2013
Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide.
Review in The New phytologist, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 267 papers.
What it found
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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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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.
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Who cites it
267 citing papers in PubMed.
- Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals.Scientific reports · 2021Trial
- Low determinism in community assembly of transient and resident pelagic fungi across climate zones in Scandinavian lakes.mSystems · 2026Article
- Influence of plant cover on the long-term dynamics of an arbuscular mycorrhizal fungal SynCom in a semi-arid Mediterranean environment.Mycorrhiza · 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
- Predicting the absence of World Health Organization fungal priority pathogens in agricultural soils using machine learning and ITS metabarcoding.Die Naturwissenschaften · 2026Article
- Bacterial and Fungal Microbiota in Anopheles darlingi Exhibit Differences in Diversity Across Three Main Colombian Malaria-endemic Regions.Microbial ecology · 2026Article
- Comparative Metabarcoding of ITS1, ITS2, and Full-Length ITS Reveals Marker- and Tissue-Specific Variation in Fungal Community Profiling in Potato.Plant-environment interactions (Hoboken, N.J.) · 2026Article
- Fungal diversity, ecology and functions in soil ecosystems.Nature reviews. Microbiology · 2026Review
- Diversity and Dispersal of Fungi Along a Subtropical Land-to-Sea Continuum.Environmental microbiology reports · 2026Article
- Sustaining Ecological Functional Zones: The Stabilizing Role of Common Fungi Against Warming Revealed by Altitudinal Transect.Journal of fungi (Basel, Switzerland) · 2026Article
- Annual Dynamics of Mycobiota in Symptomatic Century-Old Trees ofJournal of fungi (Basel, Switzerland) · 2026Article
- Contrasting elevational patterns of soil and root-associated fungal communities highlight host-driven filtering inFrontiers in plant science · 2026Article
- Microbial communities associated with two populations of the spongeBiodiversity data journal · 2026Article
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- Morphology and multi-locus phylogeny reveal three newMycoKeys · 2026Article
- Culture-based inventory and functional guild analysis of root-invading fungi associated with grassland plants across multiple regions in China.Frontiers in plant science · 2026Article
- Diversity and composition of root-associated fungal communities in critically small population ofFrontiers in plant science · 2026Article
- From Sampling to Identification of Arbuscular Mycorrhizal Fungi Through Next Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Phytomycobiomes and Ecosystem Services: Mechanisms, Evidence and Routes to Application.Journal of fungi (Basel, Switzerland) · 2025Review
- Size-fractionated fungal communities in the sunlit ocean.Communications biology · 2025Article
207 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
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
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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.