Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Denatonium-induced sinonasal bacterial killing may play a role in chronic rhinosinusitis outcomes

(2017) Ryan M. Carey et al.   International Forum of Allergy & Rhinology

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping

(2017) Katherine R. M. Mackey et al.   Frontiers in Microbiology

Microbiome of the Paranasal Sinuses: Update and Literature Review

(2016) Jivianne T. Lee et al.   American Journal of Rhinology & Allergy

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

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

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

(2016) Josef Wagner et al.   BMC MICROBIOLOGY

High-resolution phylogenetic microbial community profiling

(2016) Esther Singer et al.   ISME Journal

Improved detection of changes in species richness in high diversity microbial communities

(2016) Amy Willis et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Metagenome-wide association studies: fine-mining the microbiome

(2016) Jun Wang et al.   NATURE REVIEWS MICROBIOLOGY

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Correlation of T2R38 taste phenotype and in vitro biofilm formation from nonpolypoid chronic rhinosinusitis patients

(2016) Nithin D. Adappa et al.   International Forum of Allergy & Rhinology

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

(2016) Nam-Phuong Nguyen et al.   npj Biofilms and Microbiomes

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

The culturome of the human nose habitats reveals individual bacterial fingerprint patterns

(2015) Ursula Kaspar et al.   ENVIRONMENTAL MICROBIOLOGY

TAS2R38genotype predicts surgical outcome in nonpolypoid chronic rhinosinusitis

(2015) Nithin D. Adappa et al.   International Forum of Allergy & Rhinology

The nasal microbiota in health and disease: variation within and between subjects

(2015) Kristi Biswas et al.   Frontiers in Microbiology

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

The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline

(2015) Jérôme Lluch et al.   PLoS One

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

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

(2014) A Murat Eren et al.   ISME Journal

Bitter and sweet taste receptors regulate human upper respiratory innate immunity

(2014) Robert J. Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

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

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

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Genetic variations in taste receptors are associated with chronic rhinosinusitis: a replication study

(2014) Leandra Mfuna Endam et al.   International Forum of Allergy & Rhinology

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

(2014) Jerome T. Babauta et al.   Frontiers in Microbiology

Contrasting the Microbiomes From Healthy Volunteers and Patients With Chronic Rhinosinusitis

(2014) Rajeev Aurora et al.   JAMA Otolaryngology-Head & Neck Surgery

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

(2014) Jun Hang et al.   Microbiome

The nasal cavity microbiota of healthy adults

(2014) Christine M Bassis et al.   Microbiome

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

The microbiome of chronic rhinosinusitis: culture, molecular diagnostics and biofilm detection

(2013) Sam Boase et al.   BMC INFECTIOUS DISEASES

National burden of antibiotic use for adult rhinosinusitis

(2013) Stephanie Shintani Smith et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

High throughput sequencing methods and analysis for microbiome research

(2013) Julia M. Di Bella et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences

(2013) Swee Hoe Ong 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

The Microbiome of the Middle Meatus in Healthy Adults

(2013) Vijay R. Ramakrishnan et al.   PLoS One

The bitter taste receptor T2R38 is an independent risk factor for chronic rhinosinusitis requiring sinus surgery

(2013) Nithin D. Adappa et al.   International Forum of Allergy & Rhinology

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

(2012) B. Liu et al.   BIOINFORMATICS

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

T2R38 taste receptor polymorphisms underlie susceptibility to upper respiratory infection

(2012) Robert J. Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis

(2012) Leah M. Feazel et al.   LARYNGOSCOPE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

Sinus Microbiome Diversity Depletion and Corynebacterium tuberculostearicum Enrichment Mediates Rhinosinusitis

(2012) N. A. Abreu et al.   Science Translational Medicine

Characterization of Bacterial Community Diversity in Chronic Rhinosinusitis Infections Using Novel Culture-independent Techniques

(2011) Franziska A. Stressmann et al.   American Journal of Rhinology & Allergy

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

(2011) Jorge Barriuso et al.   BMC BIOINFORMATICS

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Biofilms in Chronic Rhinosinusitis with Nasal Polyps

(2011) Thiago Freire Pinto Bezerra et al.   OTOLARYNGOLOGY-HEAD AND NECK SURGERY

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Exploring internal features of 16S rRNA gene for identification of clinically relevant species of the genus Streptococcus

(2011) Devi Lal et al.   Annals of Clinical Microbiology and Antimicrobials

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

(2010) Minseok Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

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

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

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes

(2008) J. A. Frank et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Beta diversity and taxonomic sufficiency: Do higher-level taxa reflect heterogeneity in species composition?

(2008) Antonio Terlizzi et al.   DIVERSITY AND DISTRIBUTIONS

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH