Exploration of the Biosynthetic Potential of the Populus Microbiome

Assembly and ecological function of the root microbiome across angiosperm plant species

(2018) Connor R. Fitzpatrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome

(2018) M. A. Cregger et al.   Microbiome

luxR Homolog-Linked Biosynthetic Gene Clusters in Proteobacteria

(2018) Carolyn A. Brotherton et al.   mSystems

A new genome-mining tool redefines the lasso peptide biosynthetic landscape

(2017) Jonathan I Tietz et al.   Nature Chemical Biology

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

Simplified and representative bacterial community of maize roots

(2017) Ben Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interkingdom signaling in plant-microbe interactions

(2017) Jinhong Kan et al.   Science China-Life Sciences

Molecules to Ecosystems: Actinomycete Natural Products In situ

(2017) Scott W. Behie et al.   Frontiers in Microbiology

Microbial Volatiles: Small Molecules with an Important Role in Intra- and Inter-Kingdom Interactions

(2017) Kristin Schulz-Bohm et al.   Frontiers in Microbiology

Plant Growth Promotion by Volatile Organic Compounds Produced by Bacillus subtilis SYST2

(2017) Hafiz A. S. Tahir et al.   Frontiers in Microbiology

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

(2017) Bram Beckers et al.   Microbiome

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage

(2017) Gajender Aleti et al.   Scientific Reports

Leader Peptide-Free In Vitro Reconstitution of Microviridin Biosynthesis Enables Design of Synthetic Protease-Targeted Libraries

(2016) Emmanuel Reyna-González et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

(2016) Sagar M. Utturkar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Insights into the Unique Phosphorylation of the Lasso Peptide Paeninodin

(2016) Shaozhou Zhu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Natural Products as Sources of New Drugs from 1981 to 2014

(2016) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Structural basis for precursor protein–directed ribosomal peptide macrocyclization

(2016) Kunhua Li et al.   Nature Chemical Biology

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity

(2016) Zachary Charlop-Powers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A LuxR Homolog in a Cottonwood Tree Endophyte That Activates Gene Expression in Response to a Plant Signal or Specific Peptides

(2016) Amy L. Schaefer et al.   mBio

Diversity of Natural Product Biosynthetic Genes in the Microbiome of the Deep Sea Sponges Inflatella pellicula, Poecillastra compressa, and Stelletta normani

(2016) Erik Borchert et al.   Frontiers in Microbiology

Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System

(2016) Collin M. Timm et al.   Frontiers in Plant Science

Root bacterial endophytes alter plant phenotype, but not physiology

(2016) Jeremiah A. Henning et al.   PeerJ

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

(2015) John A. Gerlt et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Discovery of microbial natural products by activation of silent biosynthetic gene clusters

(2015) Peter J. Rutledge et al.   NATURE REVIEWS MICROBIOLOGY

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

(2015) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

(2015) Marcel Huntemann et al.   Standards in Genomic Sciences

Global biogeographic sampling of bacterial secondary metabolism

(2015) Zachary Charlop-Powers et al.   eLife

Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

(2015) Collin M. Timm et al.   Frontiers in Microbiology

Harnessing the Evolvability of Tricyclic Microviridins To Dissect Protease-Inhibitor Interactions

(2014) Annika R. Weiz et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

(2014) Aleksandr Milshteyn et al.   CHEMISTRY & BIOLOGY

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

(2014) Gregory Bonito et al.   MOLECULAR ECOLOGY

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Towards a holistic understanding of the beneficial interactions across thePopulusmicrobiome

(2014) Stéphane Hacquard et al.   NEW PHYTOLOGIST

Terpene synthases are widely distributed in bacteria

(2014) Yuuki Yamada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

Chemical Signaling Between Plants and Plant-Pathogenic Bacteria

(2013) Vittorio Venturi et al.   Annual Review of Phytopathology

LuxR- and LuxI-Type Quorum-Sensing Circuits Are Prevalent in Members of the Populus deltoides Microbiome

(2013) Amy L. Schaefer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional Analysis of Environmental DNA-Derived Microviridins Provides New Insights into the Diversity of the Tricyclic Peptide Family

(2013) Douglas Gatte-Picchi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees

(2013) Migun Shakya et al.   PLoS One

Biotic acts of antibiotics

(2013) Rustam I. Aminov   Frontiers in Microbiology

Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

(2012) Boojala Vijay B. Reddy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides

(2012) S. D. Brown et al.   JOURNAL OF BACTERIOLOGY

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

(2012) S. D. Brown et al.   JOURNAL OF BACTERIOLOGY

Pseudomonas fluorescensInduces Strain-Dependent and Strain-Independent Host Plant Responses in Defense Networks, Primary Metabolism, Photosynthesis, and Fitness

(2012) David J. Weston et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

The rhizosphere microbiome and plant health

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

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

(2011) Neil R. Gottel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Alternative Actions for Antibiotics

(2011) W. C. Ratcliff et al.   SCIENCE

Exploiting the Natural Diversity of Microviridin Gene Clusters for Discovery of Novel Tricyclic Depsipeptides

(2010) N. Ziemert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Isolation and Characterization of Two Members of the Siderophore-Microcin Family, Microcins M and H47

(2009) G. Vassiliadis et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Soil Microbial Community Responses to Multiple Experimental Climate Change Drivers

(2009) H. F. Castro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PpoR is a conserved unpaired LuxR solo of Pseudomonas putida which binds N-acyl homoserine lactones

(2009) Sujatha Subramoni et al.   BMC MICROBIOLOGY

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins

(2009) Lakshminarayan M. Iyer et al.   Molecular BioSystems

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

(2009) Stéphane Compant et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ribosomal Synthesis of Tricyclic Depsipeptides in Bloom-Forming Cyanobacteria

(2008) Nadine Ziemert et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Antibiotics as signals that trigger specific bacterial responses

(2008) Alicia Fajardo et al.   CURRENT OPINION IN MICROBIOLOGY

AHL-driven quorum-sensing circuits: their frequency and function among the Proteobacteria

(2008) Rebecca J Case et al.   ISME Journal