Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England

Spatial and temporal patterns in symptom expression within eight woodlands affected by Acute Oak Decline

(2016) Nathan Brown et al.   FOREST ECOLOGY AND MANAGEMENT

FlowClus: efficiently filtering and denoising pyrosequenced amplicons

(2015) John M Gaspar et al.   BMC BIOINFORMATICS

A Review of Polyphenolics in Oak Woods

(2015) Bo Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

(2015) Chris CR Smith et al.   ISME Journal

Combined amendment of immobilizers and the plant growth-promoting strain Burkholderia phytofirmans PsJN favours plant growth and reduces heavy metal uptake

(2015) María Touceda-González et al.   SOIL BIOLOGY & BIOCHEMISTRY

Response of leaf endophytic bacterial community to elevated CO2 at different growth stages of rice plant

(2015) Gaidi Ren et al.   Frontiers in Microbiology

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole

(2015) Xuwang Zhang et al.   PLoS One

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

(2014) Suzanne M. Prober et al.   ECOLOGY LETTERS

Spatial structuring of bacterial communities within individualGinkgo bilobatrees

(2014) Jonathan W. Leff et al.   ENVIRONMENTAL MICROBIOLOGY

Community fingerprinting in a sequencing world

(2014) Josie van Dorst et al.   FEMS MICROBIOLOGY ECOLOGY

A description of the symptoms of Acute Oak Decline in Britain and a comparative review on causes of similar disorders on oak in Europe

(2014) S. Denman et al.   FORESTRY

Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems

(2014) Delphine Lallias et al.   ISME Journal

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

(2014) S. W. Kembel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella

(2014) Carrie Brady et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Description of Brenneria roseae sp. nov. and two subspecies, Brenneria roseae subspecies roseae ssp. nov and Brenneria roseae subspecies americana ssp. nov. isolated from symptomatic oak

(2014) Carrie Brady et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Gibbsiella greigii sp. nov., a novel species associated with oak decline in the USA

(2014) Carrie Brady et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

(2014) Natacha Bodenhausen et al.   PLoS Genetics

Unraveling the plant microbiome: looking back and future perspectives

(2014) Gabriele Berg et al.   Frontiers in Microbiology

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

(2014) Jai Ram Rideout et al.   PeerJ

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

(2013) Andrea R Ottesen et al.   BMC MICROBIOLOGY

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

(2013) Jonathan W. Leff et al.   PLoS One

Quantitatively Different, yet Qualitatively Alike: A Meta-Analysis of the Mouse Core Gut Microbiome with a View towards the Human Gut Microbiome

(2013) Lukasz Krych et al.   PLoS One

Random Sampling Process Leads to Overestimation of  -Diversity of Microbial Communities

(2013) J. Zhou et al.   mBio

Diversity, distribution and sources of bacteria in residential kitchens

(2012) Gilberto E. Flores et al.   ENVIRONMENTAL MICROBIOLOGY

Culturing a plant microbiome community at the cross-Rhodes

(2012) Sarah L. Lebeis et al.   NEW PHYTOLOGIST

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 rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?

(2012) Daniel Lundin et al.   Environmental Microbiology Reports

Geographical Location Determines the Population Structure in Phyllosphere Microbial Communities of a Salt-Excreting Desert Tree

(2011) Omri M. Finkel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of Subsampling-Based Normalization Strategies for Tagged High-Throughput Sequencing Data Sets from Gut Microbiomes

(2011) Daniel Aguirre de Cárcer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring 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

Proposal to reclassify Brenneria quercina (Hildebrand and Schroth 1967) Hauben et al. 1999 into a new genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiae as Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii

(2011) C. L. Brady et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Brenneria goodwinii sp. nov., associated with acute oak decline in the UK

(2011) S. Denman et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Two decades of describing the unseen majority of aquatic microbial diversity

(2011) LUCIE ZINGER et al.   MOLECULAR ECOLOGY

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Spiroplasmas and phytoplasmas: Microbes associated with plant hosts

(2010) Gail E. Gasparich   BIOLOGICALS

PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa

(2010) Nicole Weinert et al.   FEMS MICROBIOLOGY ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price 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

Description of Gibbsiella quercinecans gen. nov., sp. nov., associated with Acute Oak Decline

(2010) Carrie Brady et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

Brenneria salicis, the bacterium causing watermark disease in willow, resides as an endophyte in wood

(2009) Martine Maes et al.   ENVIRONMENTAL MICROBIOLOGY

Robinsoniella peoriensis gen. nov., sp. nov., isolated from a swine-manure storage pit and a human clinical source

(2009) M. A. Cotta et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

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

Pseudomonas syringae pv. aesculi associated with horse chestnut bleeding canker in Germany

(2008) O. Schmidt et al.   FOREST PATHOLOGY

Phyllosphere microbiology with special reference to diversity and plant genotype

(2008) J.M. Whipps et al.   JOURNAL OF APPLIED MICROBIOLOGY

Isolation and identification of Pseudomonas syringae pv. aesculi causing bleeding canker of horse chestnut in the UK

(2008) J. F. Webber et al.   PLANT PATHOLOGY

A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes

(2008) Jörg Peplies et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Properties of bacterial endophytes and their proposed role in plant growth

(2008) Pablo R. Hardoim et al.   TRENDS IN MICROBIOLOGY