Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

Intricacies of assessing the human microbiome in epidemiologic studies

(2016) Courtney K. Robinson et al.   ANNALS OF EPIDEMIOLOGY

Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience

(2016) Benjamin C. Fu et al.   ANNALS OF EPIDEMIOLOGY

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

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

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans

(2016) Tommi Vatanen et al.   CELL

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability

(2016) Andreas Hiergeist et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

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

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods

(2016) Patrick D. Schloss   mSystems

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

(2016) Se Jin Song et al.   mSystems

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

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

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies

(2015) Vincent Thomas et al.   Future Microbiology

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data

(2015) Kaisa Koskinen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Transcriptional profiles of laccase genes in the brown rot fungus Postia placenta MAD-R-698

(2015) Hongde An et al.   JOURNAL OF MICROBIOLOGY

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

(2015) Brett Wagner Mackenzie et al.   Frontiers in Microbiology

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Advancing the Microbiome Research Community

(2014) Curtis Huttenhower et al.   CELL

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

(2014) Thomas S. B. Schmidt et al.   ENVIRONMENTAL MICROBIOLOGY

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles

(2014) Jun Hang et al.   Microbiome

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

(2014) Douglas W Fadrosh et al.   Microbiome

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model

(2013) Jonathan McCafferty et al.   ISME Journal

Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model

(2013) Julie A.K. McDonald et al.   JOURNAL OF MICROBIOLOGICAL METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

(2013) John M. Gaspar et al.   PLoS One

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel 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

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Deep Sequencing Analyses of Low Density Microbial Communities: Working at the Boundary of Accurate Microbiota Detection

(2012) Giske Biesbroek et al.   PLoS One

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

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

(2011) Daniel McDonald et al.   ISME Journal

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

(2010) Jenna L. Morgan et al.   PLoS One

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

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