Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1

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

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing

(2014) Michael A Quail et al.   BMC GENOMICS

The Unculturables: targeted isolation of bacterial species associated with canine periodontal health or disease from dental plaque

(2014) Ian J Davis et al.   BMC MICROBIOLOGY

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

(2014) Alba Santiago et al.   BMC MICROBIOLOGY

Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome

(2014) Amir Zarrinpar et al.   Cell Metabolism

Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics

(2014) Grégory Dubourg et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

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

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

Data analysis for 16S microbial profiling from different benchtop sequencing platforms

(2014) Victor S. Pylro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

How to Deal with PCR Contamination in Molecular Microbial Ecology

(2014) Adèle Mennerat et al.   MICROBIAL ECOLOGY

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li 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

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith 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

Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa

(2014) Liang Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing

(2014) Loreto Abusleme et al.   Journal of Oral Microbiology

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

(2014) Agata Wesolowska-Andersen et al.   Microbiome

Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample

(2013) A. Pfleiderer et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics

(2013) G. Dubourg et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Molecular Studies Neglect Apparently Gram-Negative Populations in the Human Gut Microbiota

(2013) P. Hugon et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Integrity of bacterial genomic DNA after autoclaving: possible implications for horizontal gene transfer and clinical waste management

(2013) J.M. Yap et al.   JOURNAL OF HOSPITAL INFECTION

Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples

(2013) Jennifer J. Mosher et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Cotranscriptional recruitment of yeast TRAMP complex to intronic sequences promotes optimal pre-mRNA splicing

(2013) Ka-Yiu Edwin Kong et al.   NUCLEIC ACIDS RESEARCH

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions

(2013) Amnon Amir et al.   NUCLEIC ACIDS RESEARCH

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

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

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

(2013) Christopher S. Miller et al.   PLoS One

Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents

(2013) Christian Hoffmann et al.   PLoS One

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

Microbial culturomics: paradigm shift in the human gut microbiome study

(2012) J.-C. Lagier 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

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Pyrosequence Read Length of 16S rRNA Gene Affects Phylogenetic Assignment of Plant-associated Bacteria

(2012) Takashi Okubo et al.   MICROBES AND ENVIRONMENTS

Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

(2012) Nastassia V. Patin et al.   MICROBIAL ECOLOGY

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic approaches to studying the human microbiota

(2012) George M. Weinstock   NATURE

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

(2012) Martin J. Sergeant et al.   PLoS One

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

(2012) Anthony A. Fodor et al.   PLoS One

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Axenic culture of fastidious and intracellular bacteria

(2012) Sudhir Singh et al.   TRENDS IN MICROBIOLOGY

Human Gut Microbiota: Repertoire and Variations

(2012) Jean-Christophe Lagier et al.   Frontiers in Cellular and Infection Microbiology

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

DNA Extraction Columns Contaminated with Murine Sequences

(2011) Otto Erlwein et al.   PLoS One

Directed Culturing of Microorganisms Using Metatranscriptomics

(2011) L. Bomar et al.   mBio

The real cost of sequencing: higher than you think!

(2011) Andrea Sboner et al.   GENOME BIOLOGY

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

Contamination of Commercial PCR Master Mix with DNA fromCoxiella burnetii

(2010) Jeroen J. H. C. Tilburg et al.   JOURNAL OF CLINICAL MICROBIOLOGY

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

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

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

(2010) Sophie Champlot et al.   PLoS One

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

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY