Community profiling of the urinary microbiota: considerations for low-biomass samples

Profiling the Urinary Microbiome in Men with Positive versus Negative Biopsies for Prostate Cancer

(2018) Eva Shrestha et al.   JOURNAL OF UROLOGY

Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women

(2018) Lesley Hoyles et al.   NATURE MEDICINE

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

(2017) Benjamin J Callahan et al.   ISME Journal

Human embryos: Collect reliable data on embryo selection

(2017) Charis Thompson   NATURE

Urinary Microbiome and Cytokine Levels in Women With Interstitial Cystitis

(2017) Melinda G. Abernethy et al.   OBSTETRICS AND GYNECOLOGY

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women

(2017) Benjamin J. Callahan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Urinary Microbiome and Psychological Factors in Women with Overactive Bladder

(2017) Peng Wu et al.   Frontiers in Cellular and Infection Microbiology

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

(2017) Mohamed Mysara et al.   GigaScience

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic

(2017) Etienne Yergeau et al.   Scientific Reports

Microbiome therapeutics — Advances and challenges

(2016) Mark Mimee et al.   ADVANCED DRUG DELIVERY REVIEWS

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

Short- and long-term effects of oral vancomycin on the human intestinal microbiota

(2016) Sandrine Isaac et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms

(2016) Travis K. Price et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Xenotransplantation 2.0

(2016)   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Antibiotic-Induced Changes in the Intestinal Microbiota and Disease

(2016) Simone Becattini et al.   TRENDS IN MOLECULAR MEDICINE

The Urinary Microbiome Differs Significantly Between Patients With Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as Between Patients With Different Clinical Phenotypes

(2016) Daniel A. Shoskes et al.   UROLOGY

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

Does the Urinary Microbiome Play a Role in Urgency Urinary Incontinence and Its Severity?

(2016) Lisa Karstens et al.   Frontiers in Cellular and Infection Microbiology

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

(2016) Evguenia Kopylova et al.   mSystems

The new world of the urinary microbiota in women

(2015) Linda Brubaker et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

The female urinary microbiome in urgency urinary incontinence

(2015) Meghan M. Pearce et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Comparison of proteases in DNA extraction via quantitative polymerase chain reaction

(2015) Alison M. Eychner et al.   ANALYTICAL BIOCHEMISTRY

How Severely Is DNA Quantification Hampered by RNA Co-extraction?

(2015) Ignacio Sanchez et al.   BIOPRESERVATION AND BIOBANKING

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

Incontinence medication response relates to the female urinary microbiota

(2015) Krystal J. Thomas-White et al.   INTERNATIONAL UROGYNECOLOGY JOURNAL

Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network

(2015) J. Curtis Nickel et al.   JOURNAL OF UROLOGY

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Optimized DNA extraction and metagenomic sequencing of airborne microbial communities

(2015) Wenjun Jiang et al.   Nature Protocols

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

How Severely Is DNA Quantification Hampered by RNA Co-extraction?

(2015) Ignacio Sanchez et al.   Biopreservation and Biobanking

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

Collection media and delayed freezing effects on microbial composition of human stool

(2015) Roberto Flores et al.   Microbiome

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

(2015) Jake Jervis-Bardy et al.   Microbiome

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

DNA/RNA Preparation for Molecular Detection

(2014) S. A. Thatcher   CLINICAL CHEMISTRY

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

(2014) Yael Haberman et al.   JOURNAL OF CLINICAL INVESTIGATION

The Female Urinary Microbiome: a Comparison of Women with and without Urgency Urinary Incontinence

(2014) M. M. Pearce et al.   mBio

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

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

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

Antibiotic Administration Routes Significantly Influence the Levels of Antibiotic Resistance in Gut Microbiota

(2013) Lu Zhang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Spectrum of Bacterial Colonization Associated with Urothelial Cells from Patients with Chronic Lower Urinary Tract Symptoms

(2013) R. Khasriya et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder

(2013) E. E. Hilt et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases

(2013) W. Dynan et al.   NUCLEIC ACIDS RESEARCH

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults

(2013) Debbie A. Lewis et al.   Frontiers in Cellular and Infection Microbiology

Alterations of microbiota in urine from women with interstitial cystitis

(2012) Huma Siddiqui et al.   BMC MICROBIOLOGY

The Role of Asymptomatic Bacteriuria in Young Women With Recurrent Urinary Tract Infections: To Treat or Not to Treat?

(2012) T. Cai et al.   CLINICAL INFECTIOUS DISEASES

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Evidence of Uncultivated Bacteria in the Adult Female Bladder

(2012) A. J. Wolfe et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury

(2012) Derrick E Fouts et al.   Journal of Translational Medicine

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

METAGENassist: a comprehensive web server for comparative metagenomics

(2012) D. Arndt et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast 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

Temporal Dynamics of the Human Vaginal Microbiota

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

Ageing of the human metaorganism: the microbial counterpart

(2011) Elena Biagi et al.   AGE

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

(2011) Huma Siddiqui et al.   BMC MICROBIOLOGY

Advancing analytical algorithms and pipelines for billions of microbial sequences

(2011) Antonio Gonzalez et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Correction: Thymosin Beta 4 Prevents Oxidative Stress by Targeting Antioxidant and Anti-Apoptotic Genes in Cardiac Fibroblasts

(2011) Sandeep Kumar et al.   PLoS One

Development of an ethidium monoazide-enhanced internally controlled universal 16S rDNA real-time polymerase chain reaction assay for detection of bacterial contamination in platelet concentrates

(2011) Poorvi Patel et al.   TRANSFUSION

Bacterial biogeography of the human digestive tract

(2011) Jennifer C. Stearns et al.   Scientific Reports

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya 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

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

(2010) Sophie Champlot et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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

Vaginal microbiome of reproductive-age women

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

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

(2010) T. Chen et al.   Database-The Journal of Biological Databases and Curation

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

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Clinical Significance of Nontraditional Bacterial Uropathogens in the Management of Chronic Prostatitis

(2008) J. Curtis Nickel et al.   JOURNAL OF UROLOGY