Novel High-Rank Phylogenetic Lineages within a Sulfur Spring (Zodletone Spring, Oklahoma), Revealed Using a Combined Pyrosequencing-Sanger Approach

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

Microbial community succession in a bioreactor modeling a souring low-temperature oil reservoir subjected to nitrate injection

(2011) Cameron M. Callbeck et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

(2011) Sébastien Monchy et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

(2011) Jennifer M. Mobberley et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Analyses of bacterial communities in meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods

(2011) Yi-Seul Kim et al.   JOURNAL OF MICROBIOLOGY

Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing

(2011) Alex J. Dumbrell et al.   NEW PHYTOLOGIST

Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison

(2011) Jiyoung Ahn et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Analysis of the bacterial community in a laboratory-scale nitrification reactor and a wastewater treatment plant by 454-pyrosequencing

(2011) Lin Ye et al.   WATER RESEARCH

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

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

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes

(2010) C. Will et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes

(2010) David L. Kirchman et al.   ENVIRONMENTAL MICROBIOLOGY

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2010) Anna Engelbrektson et al.   ISME Journal

Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments

(2010) Emily B Hollister et al.   ISME Journal

PANGEA: pipeline for analysis of next generation amplicons

(2010) Adriana Giongo et al.   ISME Journal

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots

(2010) Daniel K. Manter et al.   MICROBIAL ECOLOGY

Bacterial diversity in a glacier foreland of the high Arctic

(2010) URSEL M.E. SCHÜTTE et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring, OK, USA): The Role of the Rare Biosphere

(2010) Noha H. Youssef et al.   PLoS One

Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys

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

Composition, variability, and temporal stability of the intestinal microbiota of the elderly

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

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

Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in biosolids

(2010) Kyle Bibby et al.   WATER RESEARCH

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil

(2010) Stéphane Uroz et al.   Environmental Microbiology Reports

Microbial Populations Responsive to Denitrification-Inducing Conditions in Rice Paddy Soil, as Revealed by Comparative 16S rRNA Gene Analysis

(2009) S. Ishii et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

The effect of sequencing errors on metagenomic gene prediction

(2009) Katharina J Hoff   BMC GENOMICS

Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland)

(2009) Hannah Halm et al.   ENVIRONMENTAL MICROBIOLOGY

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA)

(2009) Annette Summers Engel et al.   ISME Journal

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

(2009) Anders F Andersson et al.   ISME Journal

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

(2009) Ryan T Jones et al.   ISME Journal

Microbial community structure in the North Pacific ocean

(2009) Mark V Brown et al.   ISME Journal

The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis

(2009) F.H. Liu et al.   JOURNAL OF APPLIED MICROBIOLOGY

Tempo-spatial patterns of bacterial community composition in the western North Pacific Ocean

(2009) Takafumi Kataoka et al.   JOURNAL OF MARINE SYSTEMS

Ecology of the rare microbial biosphere of the Arctic Ocean

(2009) Pierre E. Galand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

(2008) M. S. Elshahed et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A renaissance for the pioneering 16S rRNA gene

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

Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean

(2008) Sander K. Heijs et al.   FEMS MICROBIOLOGY ECOLOGY

Bacterial Communities Inside and Surrounding Soil Iron-Manganese Nodules

(2008) Jizheng He et al.   GEOMICROBIOLOGY JOURNAL

The rational exploration of microbial diversity

(2008) Christopher Quince et al.   ISME Journal

Distantly sampled soils carry few species in common

(2008) Roberta R Fulthorpe et al.   ISME Journal

Species richness in soil bacterial communities: A proposed approach to overcome sample size bias

(2008) Noha H. Youssef et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

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

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

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH