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

Quality control of microbiota metagenomics by k-mer analysis

(2015) Florian Plaza Onate et al.   BMC GENOMICS

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform

(2015) Yoon-Seong Jeon et al.   JOURNAL OF MICROBIOLOGY

High-Throughput Sequencing Technologies

(2015) Jason A. Reuter et al.   MOLECULAR CELL

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

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

(2015) Fiona Fouhy et al.   PLoS One

Effect of Metformin on Metabolic Improvement and Gut Microbiota

(2014) Heetae Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Processing faecal samples: a step forward for standards in microbial community analysis

(2014) Alba Santiago et al.   BMC MICROBIOLOGY

Comparison of methods for fecal microbiome biospecimen collection

(2014) Christine Dominianni et al.   BMC MICROBIOLOGY

Antibiotic treatments and microbes in the gut

(2014) Sandra Macfarlane   ENVIRONMENTAL MICROBIOLOGY

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

How many16S-based studies should be included in a metagenomic conference? It may be a matter of etymology

(2014) Alfonso Esposito et al.   FEMS MICROBIOLOGY LETTERS

Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

(2014) Jason M. Norman et al.   GASTROENTEROLOGY

Exercise and associated dietary extremes impact on gut microbial diversity

(2014) Siobhan F Clarke et al.   GUT

Improved performance of the PacBio SMRT technology for 16S rDNA sequencing

(2014) Jennifer J. Mosher et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Technology: The $1,000 genome

(2014) Erika Check Hayden   NATURE

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   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

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of quality control approaches for metagenomic data analysis

(2014) Qian Zhou et al.   Scientific Reports

Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility

(2014) Charlie T Seto et al.   Microbiome

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

(2014) Jun Hang et al.   Microbiome

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly 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

The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations

(2014) Nuria Salazar et al.   Frontiers in Genetics

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

(2013) Dong-Lei Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Demonstration of a Frozen Sample Aliquotter to Prepare Plasma and Serum Aliquots Without Thawing Frozen Parent Samples

(2013) Helena Judge Ellis et al.   BIOPRESERVATION AND BIOBANKING

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples

(2013) Shantelle Claassen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Resident viruses and their interactions with the immune system

(2013) Breck A Duerkop et al.   NATURE IMMUNOLOGY

First FDA Authorization for Next-Generation Sequencer

(2013) Francis S. Collins et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Smoking Cessation Induces Profound Changes in the Composition of the Intestinal Microbiota in Humans

(2013) Luc Biedermann et al.   PLoS One

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

The Approach to Sample Acquisition and Its Impact on the Derived Human Fecal Microbiome and VOC Metabolome

(2013) Robin D. Couch et al.   PLoS One

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

(2013) George R. Feehery et al.   PLoS One

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Study of the Viral and Microbial Communities Associated With Crohn’s Disease: A Metagenomic Approach

(2013) Vicente Pérez-Brocal et al.   Clinical and Translational Gastroenterology

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Storage conditions of intestinal microbiota matter in metagenomic analysis

(2012) Silvia Cardona et al.   BMC MICROBIOLOGY

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

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study

(2012) Roberto Flores et al.   Journal of Translational Medicine

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Developing a metagenomic view of xenobiotic metabolism

(2012) Henry J. Haiser et al.   PHARMACOLOGICAL RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

(2012) Michiel Vos et al.   PLoS One

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

(2012) Giske Biesbroek et al.   PLoS One

Variable Copy Number, Intra-Genomic Heterogeneities and Lateral Transfers of the 16S rRNA Gene in Pseudomonas

(2012) Josselin Bodilis et al.   PLoS One

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

(2012)   PLoS One

Butyrate and Propionate Protect against Diet-Induced Obesity and Regulate Gut Hormones via Free Fatty Acid Receptor 3-Independent Mechanisms

(2012) Hua V. Lin et al.   PLoS One

A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters

(2012) Susan M. Huse et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   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

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

A Crypt-Specific Core Microbiota Resides in the Mouse Colon

(2012) T. Pedron et al.   mBio

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples

(2011) Bartholomeus van den Bogert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

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

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

Abundance and diversity of mucosa-associated hydrogenotrophic microbes in the healthy human colon

(2011) Gerardo M Nava et al.   ISME Journal

Comparison of the QIAsymphony automated nucleic acid extraction and PCR setup platforms with NucliSens easyMAG and Corbett CAS-1200 liquid handling station for the detection of enteric pathogens in fecal samples

(2011) E. van Zanten et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

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

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

Improvement of the Representation of Bifidobacteria in Fecal Microbiota Metagenomic Libraries by Application of the cpn60 Universal Primer Cocktail

(2010) J. E. Hill et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

(2010) Christian L. Lauber et al.   FEMS MICROBIOLOGY LETTERS

Functional biostructure of colonic microbiota (central fermenting area, germinal stock area and separating mucus layer) in healthy subjects and patients with diarrhea treated with Saccharomyces boulardii

(2010) A. Swidsinski et al.   GASTROENTEROLOGIE CLINIQUE ET BIOLOGIQUE

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

(2010) Anne Salonen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities

(2008) Alan W. Walker et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

(2008) Johan Dicksved et al.   ISME Journal

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

(2008) Chaysavanh Manichanh et al.   NUCLEIC ACIDS RESEARCH

rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea

(2008) Z. M.-P. Lee et al.   NUCLEIC ACIDS RESEARCH