Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

Biochar alters the soil microbiome and soil function: results of next-generation amplicon sequencing across Europe

(2016) Joseph R. Jenkins et al.   Global Change Biology Bioenergy

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability

(2016) Andreas Hiergeist et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome

(2016) Bram Beckers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

(2016) Sofie Thijs et al.   Frontiers in Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill

(2015) Terrence H. Bell et al.   ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Seasonal Community Succession of the Phyllosphere Microbiome

(2015) Julia K. Copeland et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

(2015) Miranda M. Hart et al.   NEW PHYTOLOGIST

The effects of the growth substrate on cultivable and total endophytic assemblages of Arabidopsis thaliana

(2015) Sascha Truyens et al.   PLANT AND SOIL

Microbiome interplay: plants alter microbial abundance and diversity within the built environment

(2015) Alexander Mahnert et al.   Frontiers in Microbiology

Cross-Kingdom Similarities in Microbiome Ecology and Biocontrol of Pathogens

(2015) Gabriele Berg et al.   Frontiers in Microbiology

Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome

(2015) Etienne Yergeau et al.   Frontiers in Microbiology

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Biotransformation of trinitrotoluene (TNT) byPseudomonasspp. isolated from a TNT-contaminated environment

(2014) Chih-Ching Chien et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data

(2013) C. E. Robertson et al.   BIOINFORMATICS

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database

(2013) Stefan Pfeiffer et al.   ENVIRONMENTAL MICROBIOLOGY

Alteration of microbial community structure affects diesel biodegradation in an Arctic soil

(2013) Terrence H. Bell et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

(2013) Etienne Yergeau et al.   ISME Journal

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

(2013) Terrence H Bell et al.   ISME Journal

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen et al.   PLoS One

The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies

(2013) Jonas Ghyselinck et al.   PLoS One

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities

(2012) Etienne Yergeau et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

(2012) R. K. Colwell et al.   Journal of Plant Ecology

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

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

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Changes in the population of seed bacteria of transgenerationally Cd-exposedArabidopsis thaliana

(2012) S. Truyens et al.   PLANT BIOLOGY

Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

(2012) Etienne Yergeau et al.   PLoS One

Soil Bacterial Diversity Screening Using Single 16S rRNA Gene V Regions Coupled with Multi-Million Read Generating Sequencing Technologies

(2012) Sotirios Vasileiadis et al.   PLoS One

Pyrosequencing Investigation into the Bacterial Community in Permafrost Soils along the China-Russia Crude Oil Pipeline (CRCOP)

(2012) Sizhong Yang et al.   PLoS One

Permanganate Oxidizable Carbon Reflects a Processed Soil Fraction that is Sensitive to Management

(2012) Steven W. Culman et al.   SOIL SCIENCE SOCIETY OF AMERICA JOURNAL

Biodiversity and Emerging Biogeography of the Neutrophilic Iron-Oxidizing Zetaproteobacteria

(2011) Sean M. McAllister et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Discovery of commonly existing anode biofilm microbes in two different wastewater treatment MFCs using FLX Titanium pyrosequencing

(2010) Tae Kwon Lee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Short term exposure to elevated trinitrotoluene concentrations induced structural and functional changes in the soil bacterial community

(2007) Emma R. Travis et al.   ENVIRONMENTAL POLLUTION