Can Targeting Non-Contiguous V-Regions With Paired-End Sequencing Improve 16S rRNA-Based Taxonomic Resolution of Microbiomes?: An In Silico Evaluation

Resource heterogeneity structures aquatic bacterial communities

(2019) Mario E. Muscarella et al.   ISME Journal

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake

(2018) Junyi Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies

(2018) Marina Panek et al.   Scientific Reports

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease

(2018) Ahmed Moustafa et al.   Clinical and Translational Gastroenterology

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling

(2018) Garold Fuks et al.   Microbiome

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes

(2018) Deepak Yadav et al.   DNA RESEARCH

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

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

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

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

(2016) Sunil Nagpal et al.   PLoS One

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences

(2015) Anirban Dutta 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

Multiple Omics Uncovers Host–Gut Microbial Mutualism During Prebiotic Fructooligosaccharide Supplementation

(2014) Tamotsu Kato et al.   DNA RESEARCH

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term

(2014) Roberto Romero et al.   Microbiome

Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis

(2014) Luz Botero et al.   Microbiome

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome

(2013) Shuiming Xiao et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

Community differentiation of the cutaneous microbiota in psoriasis

(2013) Alexander V Alekseyenko et al.   Microbiome

Complex sputum microbial composition in patients with pulmonary tuberculosis

(2012) Zelin Cui et al.   BMC MICROBIOLOGY

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences

(2012) David A W Soergel et al.   ISME Journal

Comparison of Next-Generation Sequencing Systems

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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

(2011) Ann L Griffen et al.   ISME Journal

V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences

(2010) Martin Hartmann et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue 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