BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters

Characterization of a sponge microbiome using an integrative genome-centric approach

(2020) J. Pamela Engelberts et al.   ISME Journal

Streptovertimycins A–H, new fasamycin-type antibiotics produced by a soil-derived Streptomyces morookaense strain

(2020) Li Yang et al.   JOURNAL OF ANTIBIOTICS

1-hydroxy-7-oxolavanducyanin and Δ7″,8″-6″-hydroxynaphthomevalin from Streptomyces sp. CPCC 203577

(2020) Shufen Li et al.   JOURNAL OF ANTIBIOTICS

Shellmycin A–D, Novel Bioactive Tetrahydroanthra-γ-Pyrone Antibiotics from Marine Streptomyces sp. Shell-016

(2020) Yong Han et al.   Marine Drugs

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

Streptomyces sp. VN1, a producer of diverse metabolites including non-natural furan-type anticancer compound

(2020) Hue Thi Nguyen et al.   Scientific Reports

Disclosing the Potential of the SARP-Type Regulator PapR2 for the Activation of Antibiotic Gene Clusters in Streptomycetes

(2020) Janina Krause et al.   Frontiers in Microbiology

Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites

(2020) Vincent Hervé et al.   PeerJ

Genome-resolved metagenomics to study co-occurrence patterns and intraspecific heterogeneity among plant pathogen metapopulations

(2020) Eric Newberry et al.   ENVIRONMENTAL MICROBIOLOGY

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

(2020) Mehmet Direnç Mungan et al.   NUCLEIC ACIDS RESEARCH

The SCIFF‐derived ranthipeptides participate in quorum sensing in solventogenic clostridia

(2020) Yunliang Chen et al.   Biotechnology Journal

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

(2020) Mark C. Walker et al.   BMC GENOMICS

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery

(2020) Alexander M. Kloosterman et al.   mSystems

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

Two new glutarimide antibiotics from Streptomyces sp. HS-NF-780

(2019) Xue-Li Zhao et al.   JOURNAL OF ANTIBIOTICS

The Integrative Human Microbiome Project

(2019)   NATURE

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

(2019) Valeria Mateo-Estrada et al.   Genome Biology and Evolution

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

(2019) Geoffrey D Hannigan et al.   NUCLEIC ACIDS RESEARCH

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

(2019) Abdoul-Razak Tidjani et al.   mBio

A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota

(2019) Liu Cao et al.   mSystems

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

(2019) Rémi Zallot et al.   BIOCHEMISTRY

A computational framework to explore large-scale biosynthetic diversity

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

Learning a functional grammar of protein domains using natural language word embedding techniques

(2019) Daniel W. A. Buchan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2019) Víctor J. Carrión et al.   SCIENCE

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria

(2019) Matthew R. Olm et al.   Science Advances

Discovery of the Tyrobetaine Natural Products and Their Biosynthetic Gene Cluster via Metabologenomics

(2018) Elizabeth I. Parkinson et al.   ACS Chemical Biology

Self-Resistance of Natural Product Producers: Past, Present, and Future Focusing on Self-Resistant Protein Variants

(2018) Khaled H. Almabruk et al.   ACS Chemical Biology

Identification and functional analysis of the aspergillic acid gene cluster in Aspergillus flavus

(2018) Matthew D. Lebar et al.   FUNGAL GENETICS AND BIOLOGY

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

(2018) Stacy Ciufo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

The long view on sequencing

(2018)   NATURE BIOTECHNOLOGY

Mining for Microbial Gems: Integrating Proteomics in the Postgenomic Natural Product Discovery Pipeline

(2018) Chao Du et al.   PROTEOMICS

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

(2018) Benjamin J. Tully et al.   Scientific Data

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

(2018) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites

(2018) Jamshid Amiri Moghaddam et al.   Scientific Reports

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

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

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

Retrospective analysis of natural products provides insights for future discovery trends

(2017) Cameron R. Pye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life

(2017) Brendan B. Larsen et al.   QUARTERLY REVIEW OF BIOLOGY

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

(2017) Bradon R. McDonald et al.   mBio

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species

(2017) Jens Christian Nielsen et al.   Nature Microbiology

Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations

(2016) Ryan A. McClure et al.   ACS Chemical Biology

Resistance Gene-Guided Genome Mining: Serial Promoter Exchanges in Aspergillus nidulans Reveal the Biosynthetic Pathway for Fellutamide B, a Proteasome Inhibitor

(2016) Hsu-Hua Yeh et al.   ACS Chemical Biology

Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

(2016) Philippe Prior et al.   BMC GENOMICS

Phylogenomic Analysis of Natural Products Biosynthetic Gene Clusters Allows Discovery of Arseno-Organic Metabolites in Model Streptomycetes

(2016) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Ralstonia solanacearum lipopeptide induces chlamydospore development in fungi and facilitates bacterial entry into fungal tissues

(2016) Joseph E Spraker et al.   ISME Journal

Complete genome sequence of Streptomyces globisporus C-1027, the producer of an enediyne antibiotic lidamycin

(2016) Xingxing Li et al.   JOURNAL OF BIOTECHNOLOGY

Gifted microbes for genome mining and natural product discovery

(2016) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Scaling laws predict global microbial diversity

(2016) Kenneth J. Locey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Iterative polyketide biosynthesis by modular polyketide synthases in bacteria

(2015) Haotong Chen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

(2015) Katherine R. Duncan et al.   CHEMISTRY & BIOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Peter Cimermancic et al.   CELL

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

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

The Genome Sequence of Streptomyces lividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island

(2013) Pablo Cruz-Morales et al.   Genome Biology and Evolution

Importance of microbial natural products and the need to revitalize their discovery

(2013) Arnold L. Demain   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Biosynthesis of natural products by microbial iterative hybrid PKS–NRPS

(2013) Katja Maria Fisch   RSC Advances

Antibiotics produced by Streptomyces

(2012) Rudi Emerson de Lima Procópio et al.   Brazilian Journal of Infectious Diseases

Biosynthesis of a Complex Yersiniabactin-Like Natural Product via themicLocus in Phytopathogen Ralstonia solanacearum

(2011) Martin F. Kreutzer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Biological Systems Discovery In Silico: Radical S-Adenosylmethionine Protein Families and Their Target Peptides for Posttranslational Modification

(2011) D. H. Haft et al.   JOURNAL OF BACTERIOLOGY

Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation

(2011) Chuming Chen et al.   PLoS One

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

(2010) Kathryn E Bushley et al.   BMC EVOLUTIONARY BIOLOGY

Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

(2010) Benoît Remenant et al.   BMC GENOMICS

Natural Products Version 2.0: Connecting Genes to Molecules

(2010) Christopher T. Walsh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Data clustering: 50 years beyond K-means

(2009) Anil K. Jain   PATTERN RECOGNITION LETTERS

Origin and evolution of operons and metabolic pathways

(2009) Marco Fondi et al.   RESEARCH IN MICROBIOLOGY