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

The Earth BioGenome Project 2020: Starting the clock

(2022) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generalizing hierarchical and variation partitioning in multiple regression and canonical analyses using the rdacca.hp R package

(2022) Jiangshan Lai et al.   Methods in Ecology and Evolution

The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species

(2021) Eva Lena F. Estensmo et al.   Molecular Ecology Resources

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

(2021) Søren M. Karst et al.   NATURE METHODS

metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality

(2021) Lucie Zinger et al.   Methods in Ecology and Evolution

Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens

(2021) Edoardo Piombo et al.   Microorganisms

In honor of John Bissett: authoritative guidelines on molecular identification of Trichoderma

(2021) Feng Cai et al.   FUNGAL DIVERSITY

User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences

(2021) Martti Vasar et al.   Molecular Ecology Resources

Multi-kingdom ecological drivers of microbiota assembly in preterm infants

(2021) Chitong Rao et al.   NATURE

To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography

(2021) Adrià Antich et al.   BMC BIOINFORMATICS

Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

(2021) T. M. Porter et al.   BMC BIOINFORMATICS

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding

(2021) Miriam I. Brandt et al.   Molecular Ecology Resources

Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities

(2021) Brendan Furneaux et al.   Molecular Ecology Resources

PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi

(2021) Zuzana Kolaříková et al.   NEW PHYTOLOGIST

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Fungal taxonomy and sequence-based nomenclature

(2021) Robert Lücking et al.   Nature Microbiology

Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia)

(2021) Liisi Talas et al.   Microorganisms

High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments

(2021) Zhi-Feng Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology

(2021) Leho Tedersoo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Swarm v3: towards tera-scale amplicon clustering

(2021) Frédéric Mahé et al.   BIOINFORMATICS

Open challenges for microbial network construction and analysis

(2021) Karoline Faust   ISME Journal

Strategies for sample labelling and library preparation in DNA metabarcoding studies

(2021) Kristine Bohmann et al.   Molecular Ecology Resources

Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment

(2021) Anastasija Zaiko et al.   Molecular Ecology Resources

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

(2021) Laura Wratten et al.   NATURE METHODS

Dissecting and tuning primer editing by proofreading polymerases

(2021) Daryl M Gohl et al.   NUCLEIC ACIDS RESEARCH

A critical perspective on interpreting amplicon sequencing data in soil ecological research

(2021) Lauren V. Alteio et al.   SOIL BIOLOGY & BIOCHEMISTRY

Air-drying and long time preservation of soil do not significantly impact microbial community composition and structure

(2021) Fang Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data

(2021) Daniel Loos et al.   Frontiers in Microbiology

Ultra-accurate microbial amplicon sequencing with synthetic long reads

(2021) Benjamin J. Callahan et al.   Microbiome

The Global Soil Mycobiome consortium dataset for boosting fungal diversity research

(2021) Leho Tedersoo et al.   FUNGAL DIVERSITY

Strong primer bias for Tulasnellaceae fungi in metabarcoding: Specific primers improve the characterization of the mycorrhizal communities of epiphytic orchids

(2021) Kento Rammitsu et al.   MYCOSCIENCE

Co‐occurrence is not evidence of ecological interactions

(2020) F. Guillaume Blanchet et al.   ECOLOGY LETTERS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

(2020) Vahid Jalili et al.   NUCLEIC ACIDS RESEARCH

Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

(2020) Camille S. Delavaux et al.   Ecology and Evolution

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S ribosomal RNA, ITS, and COI marker genes

(2020) Haris Zafeiropoulos et al.   GigaScience

Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

(2020) Leho Tedersoo et al.   FUNGAL DIVERSITY

Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples

(2020) Christian Carøe et al.   Molecular Ecology Resources

Detection of base analogs incorporated during DNA replication by nanopore sequencing

(2020) Daniela Georgieva et al.   NUCLEIC ACIDS RESEARCH

Analysis of compositions of microbiomes with bias correction

(2020) Huang Lin et al.   Nature Communications

Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

(2020) Lukas Beule et al.   PeerJ

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies

(2020) Tomáš Větrovský et al.   Scientific Data

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

(2020) Teresita M. Porter et al.   Frontiers in Ecology and Evolution

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units

(2020) Lisa Joos et al.   BMC GENOMICS

Effects of soil preservation for biodiversity monitoring using environmental DNA

(2020) Alessia Guerrieri et al.   MOLECULAR ECOLOGY

Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil

(2020) Rubén López-Mondéjar et al.   SOIL BIOLOGY & BIOCHEMISTRY

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

(2020) Daniel Straub et al.   Frontiers in Microbiology

Regional-Scale In-Depth Analysis of Soil Fungal Diversity Reveals Strong pH and Plant Species Effects in Northern Europe

(2020) Leho Tedersoo et al.   Frontiers in Microbiology

Utility of large subunit for environmental sequencing of arbuscular mycorrhizal fungi: a new reference database and pipeline

(2020) Camille S. Delavaux et al.   NEW PHYTOLOGIST

You must choose, but choose wisely: Model-based approaches for microbial community analysis

(2020) Márcio F.A. Leite et al.   SOIL BIOLOGY & BIOCHEMISTRY

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results

(2020) Alejandro Abdala Asbun et al.   Frontiers in Genetics

Analysis of microbial compositions: a review of normalization and differential abundance analysis

(2020) Huang Lin et al.   npj Biofilms and Microbiomes

The Taxon Hypothesis Paradigm—On the Unambiguous Detection and Communication of Taxa

(2020) Urmas Kõljalg et al.   Microorganisms

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

(2019) Krista M. Ruppert et al.   Global Ecology and Conservation

Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform

(2019) Johanna B. Holm et al.   mSystems

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

Fungi in the Marine Environment: Open Questions and Unsolved Problems

(2019) Anthony Amend et al.   mBio

Fungi in aquatic ecosystems

(2019) Hans-Peter Grossart et al.   NATURE REVIEWS MICROBIOLOGY

Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome

(2019) Leticia Pérez‐Izquierdo et al.   JOURNAL OF ECOLOGY

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions

(2019) Lucie Zinger et al.   MOLECULAR ECOLOGY

A guide to the application of Hill numbers to DNA‐based diversity analyses

(2019) Antton Alberdi et al.   Molecular Ecology Resources

Application of Machine Learning in Microbiology

(2019) Kaiyang Qu et al.   Frontiers in Microbiology

Hierarchical generalized additive models in ecology: an introduction with mgcv

(2019) Eric J. Pedersen et al.   PeerJ

The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

(2019) Marc A. Sze et al.   mSphere

Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes

(2019) Mitsuhiko P Sato et al.   DNA RESEARCH

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution

(2019) Julien Roy et al.   NEW PHYTOLOGIST

Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data

(2019) Grace Yoon et al.   Frontiers in Genetics

From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices?

(2019) Irene Calderón‐Sanou et al.   JOURNAL OF BIOGEOGRAPHY

gllvm ‐ Fast analysis of multivariate abundance data with generalized linear latent variable models in R

(2019) Jenni Niku et al.   Methods in Ecology and Evolution

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

Host availability drives distributions of fungal endophytes in the imperilled boreal realm

(2019) Jana M. U’Ren et al.   Nature Ecology & Evolution

Reintroducing mothur: 10 years later

(2019) Patrick D. Schloss   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens

(2019) Kaire Loit et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2019) Amy E. Zanne et al.   BIOLOGICAL REVIEWS

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

(2019) Loïc Chalmandrier et al.   ECOGRAPHY

A practical guide to sample preservation and pre‐PCR processing of aquatic environmental DNA

(2019) Girish Kumar et al.   Molecular Ecology Resources

The role of multiple global change factors in driving soil functions and microbial biodiversity

(2019) Matthias C. Rillig et al.   SCIENCE

Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi

(2019) Aurélie Chambouvet et al.   CURRENT BIOLOGY

From metabarcoding to metaphylogeography: separating the wheat from the chaff

(2019) Xavier Turon et al.   ECOLOGICAL APPLICATIONS

Extracellular DNA in natural environments: features, relevance and applications

(2018) Magdalena Nagler et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2018) Tomáš Větrovský et al.   BIOINFORMATICS

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

(2018) Leho Tedersoo et al.   FUNGAL DIVERSITY

Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing

(2018) Cameron Patrick Egan et al.   Fungal Ecology

The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative

(2018) Josep Piñol et al.   MOLECULAR ECOLOGY

A fungal mock community control for amplicon sequencing experiments

(2018) Matthew G. Bakker   Molecular Ecology Resources

Towards robust and repeatable sampling methods in eDNA-based studies

(2018) Ian A. Dickie et al.   Molecular Ecology Resources

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Computational correction of index switching in multiplexed sequencing libraries

(2018) Anton J M Larsson et al.   NATURE METHODS

Probing promise versus performance in longer read fungal metabarcoding

(2018) Peter G. Kennedy et al.   NEW PHYTOLOGIST

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Stable-Isotope Probing of Human and Animal Microbiome Function

(2018) David Berry et al.   TRENDS IN MICROBIOLOGY

How, When, and Where Relic DNA Affects Microbial Diversity

(2018) J. T. Lennon et al.   mBio

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

(2018) Jonathan M. Palmer et al.   PeerJ

The state of OA: a large-scale analysis of the prevalence and impact of Open Access articles

(2018) Heather Piwowar et al.   PeerJ

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton 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

Methods for phylogenetic analysis of microbiome data

(2018) Alex D. Washburne et al.   Nature Microbiology

The value of environmental DNA biobanking for long-term biomonitoring

(2018) Simon N. Jarman et al.   Nature Ecology & Evolution

Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation

(2018) Melania E. Cristescu et al.   Annual Review of Ecology Evolution and Systematics

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

(2018) Felix Heeger et al.   Molecular Ecology Resources

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Protax -fungi: a web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences

(2018) Kessy Abarenkov et al.   NEW PHYTOLOGIST

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

(2018) Pierre Barbera et al.   SYSTEMATIC BIOLOGY

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

(2018) Sten Anslan et al.   MycoKeys

Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

(2018) Sydney I. Glassman et al.   mSphere

Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China

(2018) Teng Yang et al.   ISME Journal

Body size determines soil community assembly in a tropical forest

(2018) Lucie Zinger et al.   MOLECULAR ECOLOGY

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

(2018) Lotus A. Lofgren et al.   MOLECULAR ECOLOGY

High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations

(2018) Leho Tedersoo et al.   Molecular Ecology Resources

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Environmental DNA Time Series in Ecology

(2018) Miklós Bálint et al.   TRENDS IN ECOLOGY & EVOLUTION

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Capturing the genetic makeup of the active microbiome in situ

(2017) Esther Singer 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

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

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Moving beyond de novo clustering in fungal community ecology

(2017) Lauren C. Cline 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

Using null models to infer microbial co-occurrence networks

(2017) Nora Connor et al.   PLoS One

A re-evaluation of dilution for eliminating PCR inhibition in soil DNA samples

(2017) Hang Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities

(2017) Hirotoshi Sato et al.   Scientific Reports

Metacoder: An R package for visualization and manipulation of community taxonomic diversity data

(2017) Zachary S. L. Foster et al.   PLoS Computational Biology

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Critical Issues in Mycobiota Analysis

(2017) Bettina Halwachs et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

A guide to phylogenetic metrics for conservation, community ecology and macroecology

(2016) Caroline M. Tucker et al.   BIOLOGICAL REVIEWS

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

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

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

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

Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone

(2016) Christopher W. Fernandez et al.   GLOBAL CHANGE BIOLOGY

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities

(2016) Anders Bjørnsgaard Aas et al.   Molecular Ecology Resources

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

(2016) Vinita Deshpande et al.   MYCOLOGIA

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition

(2016) Carles Castaño 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

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community

(2016) Vendula Brabcová et al.   NEW PHYTOLOGIST

Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism"

(2016) T. D. Bruns et al.   SCIENCE

Digital identifiers for fungal species

(2016) U. Kõljalg et al.   SCIENCE

Fungal identification biases in microbiome projects

(2016) Leho Tedersoo et al.   Environmental Microbiology Reports

Temperature mediates continental-scale diversity of microbes in forest soils

(2016) Jizhong Zhou et al.   Nature Communications

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

(2016) Andrew Bissett et al.   GigaScience

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

(2016) Jennifer Fouquier et al.   Microbiome

Efficacy Assessment of Nucleic Acid Decontamination Reagents Used in Molecular Diagnostic Laboratories

(2016) Melina Fischer et al.   PLoS One

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments

(2015) Constantinos Tsirogiannis et al.   ECOGRAPHY

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

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

(2015) Alena K. Oliver et al.   Fungal Ecology

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure

(2015) Hong Qian et al.   Journal of Plant Ecology

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

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

DNA sequence-based identification of Fusarium: Current status and future directions

(2015) Kerry O’Donnell et al.   PHYTOPARASITICA

Effort versus Reward: Preparing Samples for Fungal Community Characterization in High-Throughput Sequencing Surveys of Soils

(2015) Zewei Song et al.   PLoS One

Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

(2015) J. Davison et al.   SCIENCE

Tara Oceans studies plankton at planetary scale

(2015) P. Bork et al.   SCIENCE

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

piecewiseSEM: Piecewise structural equation modelling inr for ecology, evolution, and systematics

(2015) Jonathan S. Lefcheck   Methods in Ecology and Evolution

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

(2015) Davide Albanese et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure

(2015) Hong Qian et al.   Journal of Plant Ecology

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

(2015) Yan He et al.   Microbiome

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

(2015) Leho Tedersoo et al.   MycoKeys

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Global biotic interactions: An open infrastructure to share and analyze species-interaction datasets

(2014) Jorrit H. Poelen et al.   Ecological Informatics

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales

(2014) Sebastian Horn et al.   ISME Journal

Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi

(2014) Jana M. U'Ren et al.   Molecular Ecology Resources

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

(2014) Mohammad Bahram 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

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

(2013) Andrea Porras-Alfaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning

(2013) D. Lee Taylor et al.   ECOLOGICAL MONOGRAPHS

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Network perspectives of ectomycorrhizal associations

(2013) Mohammad Bahram et al.   Fungal Ecology

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales

(2013) Mohammad Bahram et al.   JOURNAL OF 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

Phylogenetic relationships among host plants explain differences in fungal species richness and community composition in ectomycorrhizal symbiosis

(2013) Leho Tedersoo et al.   NEW PHYTOLOGIST

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

(2013) Akifumi S. Tanabe et al.   PLoS One

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

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

Estimating the Number of Species in Microbial Diversity Studies

(2013) John Bunge et al.   Annual Review of Statistics and Its Application

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

(2013) James Robert White et al.   Microbiome

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

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

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities

(2012) Jae-Hyung Ahn et al.   JOURNAL OF MICROBIOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast 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

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

(2012) N. B. Zimmerman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

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

(2012) R. Henrik Nilsson et al.   MycoKeys

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

(2011) Daniel Aguirre de Cárcer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

A novel statistical method for classifying habitat generalists and specialists

(2011) Robin L. Chazdon et al.   ECOLOGY

Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions

(2011) Greg W. Douhan et al.   Fungal Biology

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

(2011) Tiina Rajala et al.   Fungal Ecology

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

(2010) Kessy Abarenkov et al.   Evolutionary Bioinformatics

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

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

(2010) M. Öpik et al.   NEW PHYTOLOGIST

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Fungi

(2009) Jason E. Stajich et al.   CURRENT BIOLOGY

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Linking above- and belowground responses to global change at community and ecosystem scales

(2009) ANITA ANTONINKA et al.   GLOBAL CHANGE BIOLOGY

How does multiple testing correction work?

(2009) William S Noble   NATURE BIOTECHNOLOGY

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

Removal of Free Extracellular DNA from Environmental Samples by Ethidium Monoazide and Propidium Monoazide

(2008) A. O. Wagner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fungal Taxa Target Different Carbon Sources in Forest Soil

(2008) China A. Hanson et al.   ECOSYSTEMS