Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts

Autometa: automated extraction of microbial genomes from individual shotgun metagenomes

(2019) Ian J Miller et al.   NUCLEIC ACIDS RESEARCH

Localized production of defence chemicals by intracellular symbionts of Haliclona sponges

(2019) Ma. Diarey Tianero et al.   Nature Microbiology

Natural Products and Synthetic Biology: Where We Are and Where We Need To Go

(2019) Sylvia Kunakom et al.   mSystems

Automated structure prediction of trans-acyltransferase polyketide synthase products

(2019) Eric J. N. Helfrich et al.   Nature Chemical Biology

A microbial factory for defensive kahalalides in a tripartite marine symbiosis

(2019) Jindong Zan et al.   SCIENCE

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

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

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Chemistry and Biological Activities of the Marine Sponges of the Genera Mycale (Arenochalina), Biemna and Clathria

(2018) Amr El-Demerdash et al.   Marine Drugs

Accessing chemical diversity from the uncultivated symbionts of small marine animals

(2018) Thomas E Smith et al.   Nature Chemical Biology

Single-bacterial genomics validates rich and varied specialized metabolism of uncultivatedEntotheonellasponge symbionts

(2018) Tetsushi Mori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

(2017) Beate M Slaby et al.   ISME Journal

25 years of serving the community with ribosomal RNA gene reference databases and tools

(2017) Frank Oliver Glöckner et al.   JOURNAL OF BIOTECHNOLOGY

Marine Sponge Natural Products with Anticancer Potential: An Updated Review

(2017) Cinzia Calcabrini et al.   Marine Drugs

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges

(2017) Gerald Lackner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonribosomal Peptides from Marine Microbes and Their Antimicrobial and Anticancer Potential

(2017) Shivankar Agrawal et al.   Frontiers in Pharmacology

Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont

(2017) Juan Lopera et al.   mSystems

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont “Candidatus Endobugula sertula”

(2016) Ian J. Miller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated ‘Entotheonella’ bacteria

(2016) Michael F Freeman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum

(2016) Stefan Spring et al.   ISME Journal

Biosynthesis of polyketides by trans-AT polyketide synthases

(2016) Eric J. N. Helfrich et al.   NATURAL PRODUCT REPORTS

Metagenomic Analysis of the Sponge Discodermia Reveals the Production of the Cyanobacterial Natural Product Kasumigamide by ‘Entotheonella’

(2016) Yu Nakashima et al.   PLoS One

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Protective tunicate endosymbiont with extreme genome reduction

(2015) Jan-Christoph Kehr et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Metabolic and evolutionary origin of actin-binding polyketides from diverse organisms

(2015) Reiko Ueoka et al.   Nature Chemical Biology

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Isolation and diversity of natural product biosynthetic genes of cultivable bacteria associated with marine sponge Mycale sp. from the coast of Fujian, China

(2014) Pei Su et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Marine Sponge Derived Natural Products between 2001 and 2010: Trends and Opportunities for Discovery of Bioactives

(2014) Mohammad Mehbub et al.   Marine Drugs

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Calyculin biogenesis from a pyrophosphate protoxin produced by a sponge symbiont

(2014) Toshiyuki Wakimoto et al.   Nature Chemical Biology

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Defensive Bacteriome Symbiont with a Drastically Reduced Genome

(2013) Atsushi Nakabachi et al.   CURRENT BIOLOGY

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Genomics-Driven Discovery of Burkholderic Acid, a Noncanonical, Cryptic Polyketide from Human PathogenicBurkholderiaSpecies

(2012) Jakob Franke et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Malleilactone, a Polyketide Synthase-Derived Virulence Factor Encoded by the Cryptic Secondary Metabolome of Burkholderia pseudomallei Group Pathogens

(2012) John B. Biggins et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Isolation, biological activity, synthesis, and medicinal chemistry of the pederin/mycalamide family of natural products

(2012) R. Adam Mosey et al.   NATURAL PRODUCT REPORTS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Genome streamlining and chemical defense in a coral reef symbiosis

(2012) J. C. Kwan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Chemical Ecology of Sponges on Caribbean Reefs: Natural Products Shape Natural Systems

(2011) Joseph R. Pawlik   BIOSCIENCE

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The pharmaceutical value of marine biodiversity for anti-cancer drug discovery

(2010) Patrick M. Erwin et al.   ECOLOGICAL ECONOMICS

1,5-Diazacyclohenicosane, a New Cytotoxic Metabolite from the Marine Sponge Mycale sp.

(2009) Laura Coello et al.   Marine Drugs

A free-standing condensation enzyme catalyzing ester bond formation in C-1027 biosynthesis

(2009) S. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection

(2008) TuAnh Nguyen et al.   NATURE BIOTECHNOLOGY