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

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves

(2020) Julian Regalado et al.   ISME Journal

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

(2020) Stien Beirinckx et al.   Microbiome

What is new and relevant for sequencing-based microbiome research? A minireview

(2019) Alena M. Fricker et al.   Journal of Advanced Research

Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass

(2019) Vincent Caruso et al.   mSystems

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

(2019) Dominik Forster et al.   ENVIRONMENTAL MICROBIOLOGY

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

(2019) Charlie Pauvert et al.   Fungal Ecology

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

(2019) Víctor J. Carrión et al.   SCIENCE

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

(2018) Leho Tedersoo et al.   FUNGAL DIVERSITY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics

(2018) Alejandra Escobar-Zepeda et al.   Scientific Reports

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

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

(2018) Sten Anslan et al.   MycoKeys

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

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

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

(2017) Benjamin J Callahan et al.   ISME Journal

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

(2017) Florine Degrune et al.   Frontiers in Microbiology

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

(2017) Robert C. Edgar   PeerJ

Farm compost amendment and non-inversion tillage improve soil quality without increasing the risk for N and P leaching

(2016) Tommy D’Hose et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection

(2016) Caroline De Tender et al.   Frontiers in Microbiology

Back to the Future of Soil Metagenomics

(2016) Joseph Nesme et al.   Frontiers in Microbiology

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses

(2015) Marie Lisandra Zepeda Mendoza et al.   BRIEFINGS IN BIOINFORMATICS

Functional overlap of the Arabidopsis leaf and root microbiota

(2015) Yang Bai et al.   NATURE

Nanopore-based Fourth-generation DNA Sequencing Technology

(2015) Yanxiao Feng et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Emergence Shapes the Structure of the Seed Microbiota

(2014) Matthieu Barret et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS