Ecology and genomics of Actinobacteria: new concepts for natural product discovery

A Deep Learning Approach to Antibiotic Discovery

(2020) Jonathan M. Stokes et al.   CELL

Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling

(2020) Elizabeth J. Culp et al.   NATURE

Lugdunomycin, an angucycline-derived molecule with unprecedented chemical architecture

(2019) Changsheng Wu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The antimicrobial potential of Streptomyces from insect microbiomes

(2019) Marc G. Chevrette et al.   Nature Communications

Cebulantin, a Cryptic Lanthipeptide Antibiotic Uncovered using Bioactivity-Coupled HiTES

(2019) Kyuho Moon et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria

(2019) Kyuho Moon et al.   ACS Chemical Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Extreme environments: microbiology leading to specialised metabolites

(2019) Ahmed M. Sayed et al.   JOURNAL OF APPLIED MICROBIOLOGY

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools

(2019) Madeleine Ernst et al.   Metabolites

Hidden antibiotics in actinomycetes can be identified by inactivation of gene clusters for common antibiotics

(2019) Elizabeth J. Culp et al.   NATURE BIOTECHNOLOGY

A Single Biosynthetic Gene Cluster Is Responsible for the Production of Bagremycin Antibiotics and Ferroverdin Iron Chelators

(2019) Loïc Martinet et al.   mBio

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

(2019) Abdoul-Razak Tidjani et al.   mBio

Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces

(2019) Marc G. Chevrette et al.   Frontiers in Microbiology

A computational framework to explore large-scale biosynthetic diversity

(2019) Jorge C. Navarro-Muñoz et al.   Nature Chemical Biology

Bacterial siderophores in community and host interactions

(2019) Jos Kramer et al.   NATURE REVIEWS MICROBIOLOGY

A metagenomic strategy for harnessing the chemical repertoire of the human microbiome

(2019) Yuki Sugimoto et al.   SCIENCE

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

(2019) Víctor J. Carrión et al.   SCIENCE

Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity

(2018) Anne van der Meij et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery

(2018) Sébastien Rigali et al.   BIOCHEMICAL PHARMACOLOGY

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

(2018) Martina Adamek et al.   BMC GENOMICS

A phylogenetic and evolutionary analysis of antimycin biosynthesis

(2018) Rebecca Joynt et al.   MICROBIOLOGY-SGM

The role of inter-species interactions in Salinispora specialized metabolism

(2018) Nastassia V. Patin et al.   MICROBIOLOGY-SGM

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

(2018) Helga U. van der Heul et al.   NATURAL PRODUCT REPORTS

Metabolic engineering of a carbapenem antibiotic synthesis pathway in Escherichia coli

(2018) Helena Shomar et al.   Nature Chemical Biology

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Regulation of specialised metabolites in Actinobacteria - expanding the paradigms

(2018) Paul A. Hoskisson et al.   Environmental Microbiology Reports

Chemical warfare between leafcutter ant symbionts and a co-evolved pathogen

(2018) Daniel Heine et al.   Nature Communications

Extending the “One Strain Many Compounds” (OSMAC) Principle to Marine Microorganisms

(2018) Stefano Romano et al.   Marine Drugs

Dereplication of microbial metabolites through database search of mass spectra

(2018) Hosein Mohimani et al.   Nature Communications

Production of Prodiginines Is Part of a Programmed Cell Death Process in Streptomyces coelicolor

(2018) Elodie Tenconi et al.   Frontiers in Microbiology

Genomic insights into specialized metabolism in the marine actinomycete Salinispora

(2017) Anne-Catrin Letzel et al.   ENVIRONMENTAL MICROBIOLOGY

Function-related replacement of bacterial siderophore pathways

(2017) Hilke Bruns et al.   ISME Journal

Upregulation and Identification of Antibiotic Activity of a Marine-Derived Streptomyces sp. via Co-Cultures with Human Pathogens

(2017) Anne Sung et al.   Marine Drugs

Chromosomal position effect influences the heterologous expression of genes and biosynthetic gene clusters in Streptomyces albus J1074

(2017) Bohdan Bilyk et al.   Microbial Cell Factories

The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery

(2017) Mohammad Alanjary et al.   NUCLEIC ACIDS RESEARCH

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

(2017) Michael A. Skinnider et al.   NUCLEIC ACIDS RESEARCH

Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

(2017) Gregory C. A. Amos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

(2017) Bradon R. McDonald et al.   mBio

Generalist species drive microbial dispersion and evolution

(2017) Sira Sriswasdi et al.   Nature Communications

Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages

(2016) Cheryl P Andam et al.   ISME Journal

Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters

(2016) Michelle A. Schorn et al.   MICROBIOLOGY-SGM

Intertwining nutrient-sensory networks and the control of antibiotic production inStreptomyces

(2016) Mia Urem et al.   MOLECULAR MICROBIOLOGY

Human commensals producing a novel antibiotic impair pathogen colonization

(2016) Alexander Zipperer et al.   NATURE

Dereplication of peptidic natural products through database search of mass spectra

(2016) Hosein Mohimani et al.   Nature Chemical Biology

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

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

Topic modeling for untargeted substructure exploration in metabolomics

(2016) Justin Johan Jozias van der Hooft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Products and the Gene Cluster Revolution

(2016) Paul R. Jensen   TRENDS IN MICROBIOLOGY

Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer

(2016) Anthony W. Goering et al.   ACS Central Science

Coordinate Regulation of Antimycin and Candicidin Biosynthesis

(2016) Thomas C. McLean et al.   mSphere

Large-Scale Metabolomics Reveals a Complex Response of Aspergillus nidulans to Epigenetic Perturbation

(2015) Jessica C. Albright et al.   ACS Chemical Biology

Taxonomy, Physiology, and Natural Products of Actinobacteria

(2015) Essaid Ait Barka et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Natural products in soil microbe interactions and evolution

(2015) Matthew F. Traxler et al.   NATURAL PRODUCT REPORTS

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

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

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

5-Alkyl-1,2,3,4-tetrahydroquinolines, New Membrane-Interacting Lipophilic Metabolites Produced by Combined Culture of Streptomyces nigrescens and Tsukamurella pulmonis

(2015) Ryosuke Sugiyama et al.   ORGANIC LETTERS

Chojalactones A–C, Cytotoxic Butanolides Isolated from Streptomyces sp. Cultivated with Mycolic Acid Containing Bacterium

(2015) Shotaro Hoshino et al.   ORGANIC LETTERS

Socially mediated induction and suppression of antibiosis during bacterial coexistence

(2015) Monica I. Abrudan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

(2015) Kai Dührkop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

The Cellobiose Sensor CebR Is the Gatekeeper of Streptomyces scabies Pathogenicity

(2015) Isolde M. Francis et al.   mBio

Global biogeographic sampling of bacterial secondary metabolism

(2015) Zachary Charlop-Powers et al.   eLife

Genome-Wide Analysis of In Vivo Binding of the Master Regulator DasR in Streptomyces coelicolor Identifies Novel Non-Canonical Targets

(2015) Magdalena A. Świątek-Połatyńska et al.   PLoS One

Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery

(2014) Samuel Bertrand et al.   BIOTECHNOLOGY ADVANCES

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

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

(2014) Mohamed S. Donia et al.   CELL

Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation

(2014) Akram Sadeghi et al.   MICROBIOLOGICAL RESEARCH

Eliciting antibiotics active against the ESKAPE pathogens in a collection of actinomycetes isolated from mountain soils

(2014) H. Zhu et al.   MICROBIOLOGY-SGM

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Functional optimization of gene clusters by combinatorial design and assembly

(2014) Michael J Smanski et al.   NATURE BIOTECHNOLOGY

A roadmap for natural product discovery based on large-scale genomics and metabolomics

(2014) James R Doroghazi et al.   Nature Chemical Biology

Bacterial solutions to multicellularity: a tale of biofilms, filaments and fruiting bodies

(2014) Dennis Claessen et al.   NATURE REVIEWS MICROBIOLOGY

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

(2014) N. Ziemert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes

(2013) James R Doroghazi et al.   BMC GENOMICS

Metagenomic Approaches for Exploiting Uncultivated Bacteria as a Resource for Novel Biosynthetic Enzymology

(2013) Micheal C. Wilson et al.   CHEMISTRY & BIOLOGY

Application of Natural Blends of Phytochemicals Derived from the Root Exudates ofArabidopsisto the Soil Reveal That Phenolic-related Compounds Predominantly Modulate the Soil Microbiome

(2013) Dayakar V. Badri et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Triggers and cues that activate antibiotic production by actinomycetes

(2013) Hua Zhu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Molecular Regulation of Antibiotic Biosynthesis in Streptomyces

(2013) G. Liu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Nitrosporeusines A and B, Unprecedented Thioester-Bearing Alkaloids from the Arctic Streptomyces nitrosporeus

(2013) Aigang Yang et al.   ORGANIC LETTERS

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

(2013) M. F. Traxler et al.   mBio

Diversity and Natural Functions of Antibiotics Produced by Beneficial and Plant Pathogenic Bacteria

(2012) Jos M. Raaijmakers et al.   Annual Review of Phytopathology

Chitin-Induced Gene Expression in Secondary Metabolic Pathways of Streptomyces coelicolor A3(2) Grown in Soil

(2012) Behnam Nazari et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chemical Perturbation of Secondary Metabolism Demonstrates Important Links to Primary Metabolism

(2012) Arryn Craney et al.   CHEMISTRY & BIOLOGY

Interspecies modulation of bacterial development through iron competition and siderophore piracy

(2012) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY

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

(2012) Davide Bulgarelli et al.   NATURE

Structure and biosynthesis of the unusual polyketide alkaloid coelimycin P1, a metabolic product of the cpk gene cluster of Streptomyces coelicolor M145

(2012) Juan Pablo Gomez-Escribano et al.   Chemical Science

Unsuspected control of siderophore production byN-acetylglucosamine in streptomycetes

(2012) Matthias Craig et al.   Environmental Microbiology Reports

Rare actinomycetes: a potential storehouse for novel antibiotics

(2011) Kavita Tiwari et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Fix the antibiotics pipeline

(2011) Matthew A. Cooper et al.   NATURE

Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

(2011) Mariana Gabriela Ghinet et al.   PLoS One

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Mycolic Acid-Containing Bacteria Induce Natural-Product Biosynthesis inStreptomycesSpecies

(2010) Hiroyasu Onaka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Morphogenetic Signaling Molecules of the Streptomycetes

(2010) Joanne M. Willey et al.   CHEMICAL REVIEWS

The Sequence of a 1.8-Mb Bacterial Linear Plasmid Reveals a Rich Evolutionary Reservoir of Secondary Metabolic Pathways

(2010) Marnix H. Medema et al.   Genome Biology and Evolution

Origins and Evolution of Antibiotic Resistance

(2010) J. Davies et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Symbiotic streptomycetes provide antibiotic combination prophylaxis for wasp offspring

(2010) Johannes Kroiss et al.   Nature Chemical Biology

Myxococcus xanthus induces actinorhodin overproduction and aerial mycelium formation by Streptomyces coelicolor

(2010) Juana Pérez et al.   Microbial Biotechnology

Antibiotic Overproduction by rpsL and rsmG Mutants of Various Actinomycetes

(2009) Y. Tanaka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Secretory production of recombinant proteins byStreptomyces

(2009) Kristof Vrancken et al.   Future Microbiology

Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12

(2009) Takeshi Hosaka et al.   NATURE BIOTECHNOLOGY

Translating metabolic exchange with imaging mass spectrometry

(2009) Yu-Liang Yang et al.   Nature Chemical Biology

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Regulation and function of root exudates

(2009) DAYAKAR V. BADRI et al.   PLANT CELL AND ENVIRONMENT

Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans

(2009) V. Schroeckh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Autoregulation of antibiotic biosynthesis by binding of the end product to an atypical response regulator

(2009) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Renaissance in antibacterial discovery from actinomycetes

(2008) R BALTZ   CURRENT OPINION IN PHARMACOLOGY

Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces

(2008) Sébastien Rigali et al.   EMBO REPORTS

Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350

(2008) Y. Ohnishi et al.   JOURNAL OF BACTERIOLOGY

Crystal Structures of the Streptomyces coelicolor TetR-Like Protein ActR Alone and in Complex with Actinorhodin or the Actinorhodin Biosynthetic Precursor (S)-DNPA

(2008) A.R. Willems et al.   JOURNAL OF MOLECULAR BIOLOGY

Rhodostreptomycins, Antibiotics Biosynthesized Following Horizontal Gene Transfer fromStreptomyces padanustoRhodococcus fascians

(2008) Kazuhiko Kurosawa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

Streptomyces morphogenetics: dissecting differentiation in a filamentous bacterium

(2008) Klas Flärdh et al.   NATURE REVIEWS MICROBIOLOGY