Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

(2022) Derek M. Bickhart et al.   NATURE BIOTECHNOLOGY

A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes

(2022) Timo Negri et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The novel genus, ‘Candidatus Phosphoribacter’, previously identified as Tetrasphaera, is the dominant polyphosphate accumulating lineage in EBPR wastewater treatment plants worldwide

(2022) C. M. Singleton et al.   ISME Journal

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

(2022) Morten Kam Dahl Dueholm et al.   Nature Communications

Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes

(2022) Athina Gavriilidou et al.   Nature Microbiology

Biosynthetic potential of the global ocean microbiome

(2022) Lucas Paoli et al.   NATURE

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

(2021) Satria A Kautsar et al.   GigaScience

Competition Sensing Changes Antibiotic Production in Streptomyces

(2021) Sanne Westhoff et al.   mBio

antiSMASH 6.0: improving cluster detection and comparison capabilities

(2021) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

(2021) Caitlin M. Singleton et al.   Nature Communications

Genomes of novel Myxococcota reveal severely curtailed machineries for predation and cellular differentiation

(2021) Chelsea L. Murphy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000T

(2021) Shilpee Pal et al.   BMC GENOMICS

Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

(2021) Valentin Waschulin et al.   ISME Journal

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

Mining and unearthing hidden biosynthetic potential

(2021) Kirstin Scherlach et al.   Nature Communications

Metagenomics Unveils Posidonia oceanica “Banquettes” as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes)

(2021) Esther Rubio-Portillo et al.   mSystems

Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation

(2021) Isabel Johnston et al.   npj Biofilms and Microbiomes

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy

(2021) Lei Liu et al.   Microbiome

Discovery of gargantulides B and C, new 52-membered macrolactones from Amycolatopsis sp. Complete absolute stereochemistry of the gargantulide family

(2021) Daniel Carretero-Molina et al.   Organic Chemistry Frontiers

Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity

(2021) Shrikant S. Mantri et al.   mSystems

The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era

(2021) Aileen Ute Geers et al.   Computational and Structural Biotechnology Journal

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community

(2021) Chuan Hao Tan et al.   npj Biofilms and Microbiomes

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

(2021) Marc W. Van Goethem et al.   Communications Biology

The Predation Strategy of Myxococcus xanthus

(2020) Susanne Thiery et al.   Frontiers in Microbiology

Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost

(2020) Yaxin Xue et al.   FEMS MICROBIOLOGY ECOLOGY

Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019

(2020) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge

(2020) Marta Nierychlo et al.   WATER RESEARCH

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

(2020) Allison M. Sharrar et al.   mBio

Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants

(2020) Marta Nierychlo et al.   Frontiers in Microbiology

BiG-FAM: the biosynthetic gene cluster families database

(2020) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats

(2020) Ray Chen et al.   Frontiers in Microbiology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease

(2019) Gajender Aleti et al.   mBio

BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs

(2019) Dmitry Meleshko et al.   GENOME RESEARCH

Marine Chitinolytic Pseudoalteromonas Represents an Untapped Reservoir of Bioactive Potential

(2019) Sara Skøtt Paulsen et al.   mSystems

The hidden enzymology of bacterial natural product biosynthesis

(2019) Thomas A. Scott et al.   Nature Reviews Chemistry

Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential

(2019) Katherine Gregory et al.   Microorganisms

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

(2019) Eric J N Helfrich et al.   Beilstein Journal of Organic Chemistry

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

The manifold roles of microbial ribosomal peptide–based natural products in physiology and ecology

(2019) Yanyan Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

(2019) Li-Gen Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A computational framework to explore large-scale biosynthetic diversity

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

MIBiG 2.0: a repository for biosynthetic gene clusters of known function

(2019) Satria A Kautsar et al.   NUCLEIC ACIDS RESEARCH

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

(2018) Cindy J. Castelle et al.   CELL

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis

(2018) Alexander Crits-Christoph et al.   NATURE

Hopanoid lipids: from membranes to plant–bacteria interactions

(2018) Brittany J. Belin et al.   NATURE REVIEWS MICROBIOLOGY

Correlating chemical diversity with taxonomic distance for discovery of natural products in myxobacteria

(2018) Thomas Hoffmann et al.   Nature Communications

Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities

(2018) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Gifted microbes for genome mining and natural product discovery

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

Natural product discovery: past, present, and future

(2016) Leonard Katz et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Iterative polyketide biosynthesis by modular polyketide synthases in bacteria

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

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

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

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange

(2014) Ralf Beer et al.   Molecular BioSystems

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Cystomanamides: Structure and Biosynthetic Pathway of a Family of Glycosylated Lipopeptides from Myxobacteria

(2014) Lena Etzbach et al.   ORGANIC LETTERS

Towards a new science of secondary metabolism

(2013) Arryn Craney et al.   JOURNAL OF ANTIBIOTICS

Diversity and abundance of phosphonate biosynthetic genes in nature

(2013) X. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Uncultured microorganisms as a source of secondary metabolites

(2010) Kim Lewis et al.   JOURNAL OF ANTIBIOTICS

Secondary Metabolites Produced by the Marine Bacterium Halobacillus salinus That Inhibit Quorum Sensing-Controlled Phenotypes in Gram-Negative Bacteria

(2008) M. E. Teasdale et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY