Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples

Viral-bacterial co-infection in Australian Indigenous children with acute otitis media

(2011) Michael J Binks et al.   BMC INFECTIOUS DISEASES

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

(2011) Brendan P. Hodkinson et al.   ENVIRONMENTAL MICROBIOLOGY

A Novel Eukaryote-Made Thermostable DNA Polymerase Which Is Free from Bacterial DNA Contamination

(2011) Hideki Niimi et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Effect of Sample Storage Conditions on Culture-Independent Bacterial Community Measures in Cystic Fibrosis Sputum Specimens

(2011) J. Zhao et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Fusobacterium nucleatum found in colon cancer tissue—could an infection cause colorectal cancer?

(2011) Katrina Ray   Nature Reviews Gastroenterology & Hepatology

Characterization of Bacteria in Biopsies of Colon and Stools by High Throughput Sequencing of the V2 Region of Bacterial 16S rRNA Gene in Human

(2011) Yukihide Momozawa et al.   PLoS One

Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

(2011) John R. Erb-Downward et al.   PLoS One

High Diversity of the Saliva Microbiome in Batwa Pygmies

(2011) Ivan Nasidze et al.   PLoS One

Bronchoalveolar lavage in children with cystic fibrosis: how many lobes should be sampled?

(2010) F. J. Gilchrist et al.   ARCHIVES OF DISEASE IN CHILDHOOD

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim

(2010) S. Balzer et al.   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

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

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Acceleration of the direct identification of Staphylococcus aureus versus coagulase-negative staphylococci from blood culture material: a comparison of six bacterial DNA extraction methods

(2010) A. J. M. Loonen et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis

(2010) Adam M Guss et al.   ISME Journal

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

The Effects from DNA Extraction Methods on the Evaluation of Microbial Diversity Associated with Human Colonic Tissue

(2010) Páraic Ó Cuív et al.   MICROBIAL ECOLOGY

The bacterial microbiota in the oral mucosa of rural Amerindians

(2010) M. Contreras et al.   MICROBIOLOGY-SGM

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Disordered Microbial Communities in Asthmatic Airways

(2010) Markus Hilty et al.   PLoS One

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

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

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

(2010) Sophie Champlot et al.   PLoS One

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities

(2010) Howard Ochman et al.   PLOS BIOLOGY

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski et al.   GENOME BIOLOGY

Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches

(2009) Ivan Nasidze et al.   ANALYTICAL BIOCHEMISTRY

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Global diversity in the human salivary microbiome

(2009) I. Nasidze et al.   GENOME RESEARCH

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Improved detection of microbial DNA after bead-beating before DNA isolation

(2009) Richard de Boer et al.   JOURNAL OF MICROBIOLOGICAL METHODS

COMPARATIVE ANALYSIS OF METHODS FOR THE PURIFICATION OF DNA FROM LOW-BIOMASS SAMPLES BASED ON TOTAL YIELD AND CONSERVED MICROBIAL DIVERSITY

(2009) MYRON T. LA DUC et al.   JOURNAL OF RAPID METHODS AND AUTOMATION IN MICROBIOLOGY

Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

(2009) Rudolph Spangler et al.   PLoS One

Development and optimization of quantitative PCR for the diagnosis of invasive aspergillosis with bronchoalveolar lavage fluid

(2008) Prasanna D Khot et al.   BMC INFECTIOUS DISEASES

A renaissance for the pioneering 16S rRNA gene

(2008) Susannah G Tringe et al.   CURRENT OPINION IN MICROBIOLOGY

The rational exploration of microbial diversity

(2008) Christopher Quince et al.   ISME Journal

Reagent decontamination to eliminate false-positives in Escherichia coli qPCR

(2008) Sarah S. Silkie et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Metagenomics

(2008) Philip Hugenholtz et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE