A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities

Multi-kingdom microbiota analyses identify bacterial–fungal interactions and biomarkers of colorectal cancer across cohorts

(2022) Ning-Ning Liu et al.   Nature Microbiology

Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

(2022) Robert H. Mills et al.   Nature Microbiology

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

(2022) Qiyun Zhu et al.   mSystems

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

(2021) Justin P Shaffer et al.   BIOTECHNIQUES

The scope and severity of white‐nose syndrome on hibernating bats in North America

(2021) Tina L. Cheng et al.   CONSERVATION BIOLOGY

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition

(2021) Clarisse Marotz et al.   mSystems

How mycorrhizal associations drive plant population and community biology

(2020) Leho Tedersoo et al.   SCIENCE

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

Role of the microbiome in human development

(2019) Maria Gloria Dominguez-Bello et al.   GUT

Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

(2019) Ben C. Scheele et al.   SCIENCE

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

(2019) Jeremiah J. Minich et al.   mSystems

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL

(2019) Berk Aykut et al.   NATURE

Effects of sampling strategy and DNA extraction on human skin microbiome investigations

(2019) Rie Dybboe Bjerre et al.   Scientific Reports

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

(2019) Qiyun Zhu et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Fungal infections in animals: a patchwork of different situations

(2018) Seyedmojtaba Seyedmousavi et al.   MEDICAL MYCOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

(2018) Stefan Janssen et al.   mSystems

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

(2018) Jeremiah J. Minich et al.   mSystems

Evolutionary history resolves global organization of root functional traits

(2018) Zeqing Ma et al.   NATURE

Qiita: rapid, web-enabled microbiome meta-analysis

(2018) Antonio Gonzalez et al.   NATURE METHODS

Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer

(2018) Olabisi Oluwabukola Coker et al.   GUT

Evaluating the Information Content of Shallow Shotgun Metagenomics

(2018) Benjamin Hillmann et al.   mSystems

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity

(2018) Jeremiah J. Minich et al.   mSystems

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

A Diverse Soil Microbiome Degrades More Crude Oil than Specialized Bacterial Assemblages Obtained in Culture

(2016) Terrence H. Bell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Crop-destroying fungal and oomycete pathogens challenge food security

(2015) Daniel P. Bebber et al.   FUNGAL GENETICS AND BIOLOGY

Fecal Microbiota Transplant for Treatment of Clostridium difficile Infection in Immunocompromised Patients

(2014) Colleen R Kelly et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Selection on soil microbiomes reveals reproducible impacts on plant function

(2014) Kevin Panke-Buisse et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The Top 10 fungal pathogens in molecular plant pathology

(2012) RALPH DEAN et al.   MOLECULAR PLANT PATHOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS