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Ecological inference and contaminant detection from fungal microbiome data with q2-fungal-traits

https://doi.org/10.64898/2026.06.17.732913

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Spore sensitivity to sunlight and freezing can restrict dispersal in wood‐decay fungi

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Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents

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The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts

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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles

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Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions

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A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors

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FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

inferredcites →https://doi.org/10.1016/j.soilbio.2013.08.027openalex-snapshot

Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution?

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Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

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Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities

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DADA2: High-resolution sample inference from Illumina amplicon data

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Microbiota in cancer: current understandings and future perspectives

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Taxonomic diversity of fungi deposited from the atmosphere

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Fungal communities decline with urbanization—more in air than in soil

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Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems

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Guidelines for preventing and reporting contamination in low-biomass microbiome studies

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The multi-kingdom cancer microbiome

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The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases

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Best practices for analysing microbiomes

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Mycobiome diversity: high-throughput sequencing and identification of fungi

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Microbial interactions and ecology in fermented food ecosystems

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Airborne DNA reveals predictable spatial and seasonal dynamics of fungi

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Fungal impacts on Earth’s ecosystems

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Global hotspots of mycorrhizal fungal richness are poorly protected

inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes

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Setting higher standards for reports of microbial species in human cancers

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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

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Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue

inferredcites →https://doi.org/10.1093/database/baaa062openalex-snapshot

NCBI Taxonomy: a comprehensive update on curation, resources and tools

inferredcites →https://doi.org/10.1093/femsre/fuab058openalex-snapshot

Fungi as mediators linking organisms and ecosystems

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Inferring microbiota functions from taxonomic genes: a review

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One hundred unanswered questions on the dispersal ecology of fungi

inferredcites →https://doi.org/10.1093/nar/gkad1039openalex-snapshot

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

inferredcites →https://doi.org/10.1093/nar/gkae959openalex-snapshot

Bac Dive in 2025: the core database for prokaryotic strain data

inferredcites →https://doi.org/10.1098/rspb.2021.0552openalex-snapshot

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

inferredcites →https://doi.org/10.1098/rspb.2023.2531openalex-snapshot

Effects of past and present habitat on the gut microbiota of a wild rodent

inferredcites →https://doi.org/10.1101/2025.01.27.635007openalex-snapshot

MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework

inferredcites →https://doi.org/10.1111/1365-2435.70043openalex-snapshot

Urbanization alters fungal functional composition in boreal ecosystems by favouring larger‐spore fungi and pathogenic fungi

inferredcites →https://doi.org/10.1111/brv.12570openalex-snapshot

Fungal functional ecology: bringing a trait‐based approach to plant‐associated fungi

inferredcites →https://doi.org/10.1111/ele.14271openalex-snapshot

Symbiotic status alters fungal eco‐evolutionary offspring trajectories

inferredcites →https://doi.org/10.1111/j.1442-9993.2001.01070.pp.xopenalex-snapshot

A new method for non‐parametric multivariate analysis of variance

inferredcites →https://doi.org/10.1111/mec.14995openalex-snapshot

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

inferredcites →https://doi.org/10.1111/mec.16460openalex-snapshot

Best practices in metabarcoding of fungi: From experimental design to results

inferredcites →https://doi.org/10.1111/mec.16754openalex-snapshot

Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils

inferredcites →https://doi.org/10.1111/nph.19283openalex-snapshot

GlobalAMFungi : a global database of arbuscular mycorrhizal fungal occurrences from high‐throughput sequencing metabarcoding studies

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The landscape of microbial associations in human cancer

inferredcites →https://doi.org/10.1126/scitranslmed.ads6335openalex-snapshot

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

inferredcites →https://doi.org/10.1128/mbio.00631-16openalex-snapshot

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

inferredcites →https://doi.org/10.1128/msystems.01550-24openalex-snapshot

Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting

inferredcites →https://doi.org/10.1146/annurev-ecolsys-012622-021604openalex-snapshot

Fungal Dispersal Across Spatial Scales

inferredcites →https://doi.org/10.1186/s40168-018-0605-2openalex-snapshot

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

inferredcites →https://doi.org/10.1186/s40168-023-01586-yopenalex-snapshot

Enterotypes of the human gut mycobiome

inferredcites →https://doi.org/10.1186/s42523-021-00134-zopenalex-snapshot

Defining gut mycobiota for wild animals: a need for caution in assigning authentic resident fungal taxa

inferredcites →https://doi.org/10.1371/journal.pbio.3003390openalex-snapshot

Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates

inferredcites →https://doi.org/10.1371/journal.pcbi.1009581openalex-snapshot

RESCRIPt: Reproducible sequence taxonomy reference database management

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.1890/13-0877.1openalex-snapshot

Do small spores disperse further than large spores?

inferredcites →https://doi.org/10.7554/elife.61644openalex-snapshot

The diversity and function of sourdough starter microbiomes

inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot

VSEARCH: a versatile open source tool for metagenomics

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1128/aem.01190-26openalex-snapshot

Microbial terroir in winegrowing: revisiting the role of microbial biogeography in terroir expression

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