Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota

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

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

(2015) Christopher L. Hemme et al.   Frontiers in 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

The Vaginal Microbiota over an 8- to 10-Year Period in a Cohort of HIV-Infected and HIV-Uninfected Women

(2015) Supriya D. Mehta et al.   PLoS One

The effects of reproductive hormones on the physical properties of cervicovaginal fluid

(2014) Catherine A. Chappell et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

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

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

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women

(2014) Hanneke Borgdorff et al.   ISME Journal

Interplay Between the Temporal Dynamics of the Vaginal Microbiota and Human Papillomavirus Detection

(2014) R. M. Brotman et al.   JOURNAL OF INFECTIOUS DISEASES

Homogeneity of the Vaginal Microbiome at the Cervix, Posterior Fornix, and Vaginal Canal in Pregnant Chinese Women

(2014) Yi-E Huang et al.   MICROBIAL ECOLOGY

Pregnancy's Stronghold on the Vaginal Microbiome

(2014) Marina R. S. Walther-António et al.   PLoS One

Bacterial Communities in Semen from Men of Infertile Couples: Metagenomic Sequencing Reveals Relationships of Seminal Microbiota to Semen Quality

(2014) Shun-Long Weng et al.   PLoS One

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

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

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

Mastering methodological pitfalls for surviving the metagenomic jungle

(2013) Tom O. Delmont et al.   BIOESSAYS

Association of the Vaginal Microbiota with Human Papillomavirus Infection in a Korean Twin Cohort

(2013) Jung Eun Lee et al.   PLoS One

Composition of the Vaginal Microbiota in Women of Reproductive Age – Sensitive and Specific Molecular Diagnosis of Bacterial Vaginosis Is Possible?

(2013) Elena Shipitsyna et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Association Between Trichomonas vaginalis and Vaginal Bacterial Community Composition Among Reproductive-Age Women

(2013) Rebecca M. Brotman et al.   SEXUALLY TRANSMITTED DISEASES

Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

(2012) Feng Guo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Altered Vaginal Microbiota Are Associated With Perinatal Mother-to-Child Transmission of HIV in African Women From Burkina Faso

(2012) Daniel N. Frank et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy

(2012) Kjersti Aagaard et al.   PLoS One

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

(2012) Dana Willner et al.   PLoS One

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

(2012) Sujatha Srinivasan et al.   PLoS One

The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization

(2012) Benjamin C. Smith et al.   PLoS One

Temporal Dynamics of the Human Vaginal Microbiota

(2012) P. Gajer et al.   Science Translational Medicine

Molecular Definition of Vaginal Microbiota in East African Commercial Sex Workers

(2011) John J. Schellenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial vaginosis is associated with uterine cervical human papillomavirus infection: a meta-analysis

(2011) Evy Gillet et al.   BMC INFECTIOUS DISEASES

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis

(2010) Xin Z Ling et al.   BMC GENOMICS

Denitrification at pH 4 by a soil-derived Rhodanobacter-dominated community

(2010) R. N. Van Den Heuvel et al.   ENVIRONMENTAL MICROBIOLOGY

Modifications to the Peptidoglycan Backbone Help Bacteria To Establish Infection

(2010) Kimberly M. Davis et al.   INFECTION AND IMMUNITY

Comparison of Self-Collected and Physician-Collected Vaginal Swabs for Microbiome Analysis

(2010) L. J. Forney 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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Deep Sequencing of the Vaginal Microbiota of Women with HIV

(2010) Ruben Hummelen et al.   PLoS One

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis

(2008) B. B. Oakley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Vaginosis and Vaginal Yeast, But Not Vaginal Cleansing, Increase HIV-1 Acquisition in African Women

(2008) Janneke H H M van de Wijgert et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES