Mycobiome diversity: high-throughput sequencing and identification of fungi

Dynamics and diversity of a microbial community during the fermentation of industrialized Qingcai paocai, a traditional Chinese fermented vegetable food, as assessed by Illumina MiSeq sequencing, DGGE and qPCR assay

(2018) Huipeng Liang et al.   ANNALS OF MICROBIOLOGY

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

(2018) Tomáš Větrovský et al.   BIOINFORMATICS

High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration

(2018) DongFeng Yan et al.   BIOLOGICAL CONSERVATION

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies

(2018) Ahmed Abdelfattah et al.   BIOLOGICAL CONTROL

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge

(2018) Wei Xu et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

High-level classification of the Fungi and a tool for evolutionary ecological analyses

(2018) Leho Tedersoo et al.   FUNGAL DIVERSITY

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots

(2018) Petr Kohout et al.   ISME Journal

What lies beneath? Fungal diversity at the bottom of Lake Michigan and Lake Superior

(2018) Hannah E. Wahl et al.   JOURNAL OF GREAT LAKES RESEARCH

Fungal infections in animals: a patchwork of different situations

(2018) Seyedmojtaba Seyedmousavi et al.   MEDICAL MYCOLOGY

A fungal mock community control for amplicon sequencing experiments

(2018) Matthew G. Bakker   Molecular Ecology Resources

Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition

(2018) Martin Unterseher et al.   MYCOLOGICAL PROGRESS

Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

(2018) Søren M Karst et al.   NATURE BIOTECHNOLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy

(2018) Elisa Banchi et al.   PLoS One

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

(2018) Jonathan M. Palmer et al.   PeerJ

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

(2018) R. Henrik Nilsson et al.   MycoKeys

Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

(2018) Robert Lücking et al.   IMA Fungus

CTAB-PEG DNA Extraction from Fungi with High Contents of Polysaccharides

(2018) X. Huang et al.   MOLECULAR BIOLOGY

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

Introducing ribosomal tandem repeat barcoding for fungi

(2018) Christian Wurzbacher et al.   Molecular Ecology Resources

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

(2018) Sten Anslan et al.   MycoKeys

Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation

(2018) D. Vu et al.   STUDIES IN MYCOLOGY

Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use

(2017) Johanna Muurinen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Fungal communities associated with bark and ambrosia beetles trapped at international harbours

(2017) Antonino Malacrinò et al.   Fungal Ecology

Fungal communities in Scandinavian lakes along a longitudinal gradient

(2017) Maryia Khomich et al.   Fungal Ecology

Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans

(2017) Christopher A. Desjardins et al.   GENOME RESEARCH

Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs

(2017) Raisa Mäkipää et al.   ISME Journal

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

(2017) S Emilia Hannula et al.   ISME Journal

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands

(2017) Julia Kyaschenko et al.   ISME Journal

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Plant species richness and productivity determine the diversity of soil fungal guilds in temperate coniferous forest and bog habitats

(2017) Indrek Hiiesalu et al.   MOLECULAR ECOLOGY

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data

(2017) Sten Anslan et al.   Molecular Ecology Resources

Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis

(2017) Allison Q. Byrne et al.   Molecular Ecology Resources

Real-time PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference?

(2017) Alena Voříšková et al.   MYCORRHIZA

Host preference and network properties in biotrophic plant-fungal associations

(2017) Sergei Põlme et al.   NEW PHYTOLOGIST

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity

(2017) Teng Yang et al.   NEW PHYTOLOGIST

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

The emerging importance and challenges of the human mycobiome

(2017) Heidi H. Kong et al.   Virulence

Critical Issues in Mycobiota Analysis

(2017) Bettina Halwachs et al.   Frontiers in Microbiology

Uncovering unseen fungal diversity from plant DNA banks

(2017) Erin M. Datlof et al.   PeerJ

Novel soil-inhabiting clades fill gaps in the fungal tree of life

(2017) Leho Tedersoo et al.   Microbiome

Population Genomics of Fungal and Oomycete Pathogens

(2016) Niklaus J. Grünwald et al.   Annual Review of Phytopathology

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

(2016) Johan Bengtsson-Palme et al.   Ecological Informatics

Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic

(2016) Brandon T. Hassett et al.   ENVIRONMENTAL MICROBIOLOGY

Specificity and localised distribution of mycorrhizal fungi in the soil may contribute to co-existence of orchid species

(2016) Michael Waud et al.   Fungal Ecology

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

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi

(2016) Hans-Peter Grossart et al.   Fungal Ecology

Fungal microbiota dysbiosis in IBD

(2016) Harry Sokol et al.   GUT

Multi-year assessment of coastal planktonic fungi reveals environmental drivers of diversity and abundance

(2016) Joe D Taylor et al.   ISME Journal

High-resolution phylogenetic microbial community profiling

(2016) Esther Singer et al.   ISME Journal

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

(2016) Alexander B Bochdansky et al.   ISME Journal

Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment

(2016) Nhu H. Nguyen et al.   MOLECULAR ECOLOGY

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

A qPCR assay that specifically quantifies Tricholoma matsutake biomass in natural soil

(2016) Muneyoshi Yamaguchi et al.   MYCORRHIZA

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Dimensions of biodiversity in the Earth mycobiome

(2016) Kabir G. Peay et al.   NATURE REVIEWS MICROBIOLOGY

High-resolution community profiling of arbuscular mycorrhizal fungi

(2016) Klaus Schlaeppi et al.   NEW PHYTOLOGIST

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome-Picea glaucasystem at an arctic treeline ecotone

(2016) Pascal Eusemann et al.   NEW PHYTOLOGIST

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Digital identifiers for fungal species

(2016) U. Kõljalg et al.   SCIENCE

A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing

(2016) Wenke Smets et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungal identification biases in microbiome projects

(2016) Leho Tedersoo et al.   Environmental Microbiology Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)

(2016) Christian Wurzbacher et al.   MycoKeys

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

(2016) Kessy Abarenkov et al.   MycoKeys

Top 50 most wanted fungi

(2016) R. Henrik Nilsson et al.   MycoKeys

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Habitat-driven variation in mycorrhizal communities in the terrestrial orchid genus Dactylorhiza

(2016) Hans Jacquemyn et al.   Scientific Reports

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis

(2015) Liyou Wu et al.   BMC MICROBIOLOGY

Neglected role of fungal community composition in explaining variation in wood decay rates

(2015) A. van der Wal et al.   ECOLOGY

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular and functional characteristics of streptomycete communities in relation to soil factors and potato common scab

(2015) Pingping Sun et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Prospects and challenges for fungal metatranscriptomics of complex communities

(2015) Cheryl R. Kuske et al.   Fungal Ecology

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

(2015) Leho Tedersoo et al.   ISME Journal

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database—the quality controlled standard tool for routine identification of human and animal pathogenic fungi

(2015) Laszlo Irinyi et al.   MEDICAL MYCOLOGY

Therpb2gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

(2015) Tomáš Větrovský et al.   Molecular Ecology Resources

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

Changes in fungal communities along a boreal forest soil fertility gradient

(2015) Erica Sterkenburg et al.   NEW PHYTOLOGIST

Common foliar fungi ofPopulus trichocarpamodifyMelampsorarust disease severity

(2015) Posy E. Busby et al.   NEW PHYTOLOGIST

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

(2015) J.B. Stielow et al.   PERSOONIA

Molecular diversity and distribution of marine fungi across 130 European environmental samples

(2015) Thomas A. Richards et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

(2015) J. Davison et al.   SCIENCE

Microbial community assembly and metabolic function during mammalian corpse decomposition

(2015) J. L. Metcalf et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

(2015) Jizhong Zhou et al.   mBio

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

(2015) Hyun S. Gweon et al.   Methods in Ecology and Evolution

Relationship between soil fungal diversity and temperature in the maritime Antarctic

(2015) Kevin K. Newsham et al.   Nature Climate Change

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

(2015) Cedar N. Hesse et al.   Frontiers in Microbiology

The Community Structures of Prokaryotes and Fungi in Mountain Pasture Soils are Highly Correlated and Primarily Influenced by pH

(2015) Anders Lanzén et al.   Frontiers in Microbiology

Standardizing metadata and taxonomic identification in metabarcoding studies

(2015) Leho Tedersoo et al.   GigaScience

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces

(2015) Gareth Wyn Griffith et al.   MycoKeys

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

(2015) Leho Tedersoo et al.   MycoKeys

Fungi Identify the Geographic Origin of Dust Samples

(2015) Neal S. Grantham et al.   PLoS One

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea)

(2015) Ahmed Abdelfattah et al.   PLoS One

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated withPiloderma-Pinussymbiosis: improved methodologies for assessing gene expressionin situ

(2014) H.-L. Liao et al.   ENVIRONMENTAL MICROBIOLOGY

Communities of fungal endophytes in tropical forest grasses: highly diverse host- and habitat generalists characterized by strong spatial structure

(2014) K. Lindsay Higgins et al.   Fungal Ecology

Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales

(2014) Sebastian Horn et al.   ISME Journal

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

When the forest dies: the response of forest soil fungi to a bark beetle-induced tree dieback

(2014) Martina Štursová et al.   ISME Journal

Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars

(2014) Miklós Bálint et al.   MOLECULAR ECOLOGY

Local-scale biogeography and spatiotemporal variability in communities of mycorrhizal fungi

(2014) Mohammad Bahram et al.   NEW PHYTOLOGIST

Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass

(2014) Inga Hiiesalu et al.   NEW PHYTOLOGIST

Fungal associations of basal vascular plants: reopening a closed book?

(2014) William R. Rimington et al.   NEW PHYTOLOGIST

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Effects of the use of biocontrol agent (Phlebiopsis gigantea) on fungal communities on the surface of Picea abies stumps

(2013) E Terhonen et al.   FOREST ECOLOGY AND MANAGEMENT

Factors shaping community structure of endophytic fungi–evidence from the Pinus-Viscum-system

(2013) Derek Peršoh   FUNGAL DIVERSITY

Fungal under-representation is (indeed) diminishing in the life sciences

(2013) Marco Pautasso   Fungal Ecology

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

(2013) Daniel L. Lindner et al.   Ecology and Evolution

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Estimation of fungal biomass in forest litter and soil

(2012) Petr Baldrian et al.   Fungal Ecology

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

(2012) Martin Hartmann et al.   ISME Journal

Fungal community on decomposing leaf litter undergoes rapid successional changes

(2012) Jana Voříšková et al.   ISME Journal

Mouse model of oropharyngeal candidiasis

(2012) Norma V Solis et al.   Nature Protocols

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

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

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

(2012) M. E. Allentoft et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evaluation of methods to estimate production, biomass and turnover of ectomycorrhizal mycelium in forests soils – A review

(2012) H. Wallander et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungi and the Rise of Mammals

(2012) Arturo Casadevall   PLoS Pathogens

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

(2012) R. Henrik Nilsson et al.   MycoKeys

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

(2011) Benjamin J. Hindson et al.   ANALYTICAL CHEMISTRY

Hidden Fungi, Emergent Properties: Endophytes and Microbiomes

(2011) Andrea Porras-Alfaro et al.   Annual Review of Phytopathology

RNA reveals a succession of active fungi during the decay of Norway spruce logs

(2011) Tiina Rajala et al.   Fungal Ecology

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian et al.   ISME Journal

Discovery of novel intermediate forms redefines the fungal tree of life

(2011) Meredith D. M. Jones et al.   NATURE

Storage of environmental samples for guaranteeing nucleic acid yields for molecular microbiological studies

(2010) Antti Juhani Rissanen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Transformation of Quercus petraea litter: successive changes in litter chemistry are reflected in differential enzyme activity and changes in the microbial community composition

(2010) Jaroslav Šnajdr et al.   FEMS MICROBIOLOGY ECOLOGY

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Massively parallel 454-sequencing of fungal communities inQuercusspp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites

(2010) ARI JUMPPONEN et al.   MOLECULAR ECOLOGY

Vertical distribution of fungal communities in tallgrass prairie soil

(2010) Ari Jumpponen et al.   MYCOLOGIA

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

(2010) A. S. Amend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development and validation of an oligonucleotide microarray to characterise ectomycorrhizal fungal communities

(2009) Marlis Reich et al.   BMC MICROBIOLOGY

Relative roles of niche and neutral processes in structuring a soil microbial community

(2009) Alex J Dumbrell et al.   ISME Journal

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Fungal ecology catches fire

(2009) David S. Hibbett et al.   NEW PHYTOLOGIST