Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory

Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics

(2018) Stefan A. Boers et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

(2018) Robert C. Edgar   PeerJ

Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses

(2018) Marcos Parras-Moltó et al.   Microbiome

Detection of Bacterial DNA in Septic Arthritis Samples Using the MYcrobiota Platform

(2018) Stefan A. Boers et al.   JCR-JOURNAL OF CLINICAL RHEUMATOLOGY

Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform

(2018) Stefan A. Boers et al.   Scientific Reports

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

(2018) Sydney I. Glassman et al.   mSphere

Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur

(2018) Saskia D Hiltemann et al.   GigaScience

Pre-implementation guidelines for infectious disease point-of-care testing in medical institutions

(2017) Annemiek A van der Eijk et al.   Future Microbiology

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

(2017) Benjamin J Callahan et al.   ISME Journal

The Microbiome and Risk for Obesity and Diabetes

(2017) Anthony L. Komaroff   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling

(2017) Stefan A. Boers et al.   Scientific Reports

Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

(2017) Xiaoli Dong et al.   Frontiers in Microbiology

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach

(2017) Bonnie L. Brown et al.   GigaScience

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis

(2017) Fiona J. Whelan et al.   Microbiome

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

(2016) Bo Yang et al.   BMC BIOINFORMATICS

Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples

(2016) Lisa A. Cummings et al.   CLINICAL CHEMISTRY

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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

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

(2016) Patrick D. Schloss et al.   PeerJ

Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

(2016) Alfonso Benítez-Páez et al.   GigaScience

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?

(2016) Alexander G. Shaw et al.   Microbiome

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

(2016) Yemin Lan et al.   Microbiome

Open-Source Sequence Clustering Methods Improve the State Of the Art

(2016) Evguenia Kopylova et al.   mSystems

Gut microbiome and innate immune response patterns in IgE-associated eczema

(2015) C. E. West et al.   CLINICAL AND EXPERIMENTAL ALLERGY

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

(2015) Jean-Christophe Lagier et al.   CLINICAL MICROBIOLOGY REVIEWS

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

Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

(2015) Leah Cuthbertson et al.   Journal of Cystic Fibrosis

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Role of the Gut Microbiome in Obesity and Diabetes Mellitus

(2015) Gillian M. Barlow et al.   NUTRITION IN CLINICAL PRACTICE

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures

(2015) Stefan A. Boers et al.   Scientific Reports

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections

(2014) L. Cuthbertson et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

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

Low gut microbiota diversity in early infancy precedes asthma at school age

(2013) T. R. Abrahamsson et al.   CLINICAL AND EXPERIMENTAL ALLERGY

Better Tests, Better Care: Improved Diagnostics for Infectious Diseases

(2013) A. M. Caliendo et al.   CLINICAL INFECTIOUS DISEASES

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Antibiotic pressure can induce the viable but non-culturable state in Staphylococcus aureus growing in biofilms

(2013) S. Pasquaroli et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

(2013) Stephen J. Salipante et al.   PLoS One

A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples

(2013) Elizabeth M. Batty et al.   PLoS One

Gut–brain axis: how the microbiome influences anxiety and depression

(2013) Jane A. Foster et al.   TRENDS IN NEUROSCIENCES

Virus discovery: one step beyond

(2013) Saskia L Smits et al.   Current Opinion in Virology

Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing

(2012) Daniel D Rhoads et al.   BMC INFECTIOUS DISEASES

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

Outbreak of Shiga Toxin-Producing Escherichia coli O104:H4 Associated With Organic Fenugreek Sprouts, France, June 2011

(2012) L. A. King et al.   CLINICAL INFECTIOUS DISEASES

Next-generation sequencing technology in clinical virology

(2012) M.R. Capobianchi et al.   CLINICAL MICROBIOLOGY AND INFECTION

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

(2012) Martin Iain Bahl et al.   FEMS MICROBIOLOGY LETTERS

Decreased abundance ofFaecalibacterium prausnitziiin the gut microbiota of Crohn's disease

(2012) Takehide Fujimoto et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing

(2012) Kathleen Sim et al.   PLoS One

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

(2012)   PLoS One

Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage

(2012) Ian M. Carroll et al.   PLoS One

Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria

(2012) V. Salman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples

(2011) Johanna Maukonen et al.   FEMS MICROBIOLOGY ECOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Identification of the Shiga Toxin-Producing Escherichia coli O104:H4 Strain Responsible for a Food Poisoning Outbreak in Germany by PCR : Table 1.

(2011) Junjie Qin et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Mechanical Disruption of Lysis-Resistant Bacterial Cells by Use of a Miniature, Low-Power, Disposable Device

(2011) Peter E. Vandeventer et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study

(2011) Martina Bielaszewska et al.   LANCET INFECTIOUS DISEASES

Discovery of novel intermediate forms redefines the fungal tree of life

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

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology

(2011) Alexander Mellmann et al.   PLoS One

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

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

A microbial detection array (MDA) for viral and bacterial detection

(2010) Shea N Gardner et al.   BMC GENOMICS

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

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

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

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The rpoB gene as a tool for clinical microbiologists

(2008) Toïdi Adékambi et al.   TRENDS IN MICROBIOLOGY