Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges

(2017) Dennis Versluis et al.   MARINE BIOTECHNOLOGY

Pseudovibrio stylochi sp. nov., isolated from a marine flatworm

(2016) Yu Zhang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink

(2016) Maxwell Z. Wilson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

(2016) Jasper J. Koehorst et al.   Scientific Reports

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

(2016) Ilias Lagkouvardos et al.   Scientific Reports

Pseudovibrio hongkongensis sp. nov., isolated from a marine flatworm

(2015) Ying Xu et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Exploring the genomic traits of fungus-feeding bacterial genus Collimonas

(2015) Chunxu Song et al.   BMC GENOMICS

A novel sponge disease caused by a consortium of micro-organisms

(2015) Michael Sweet et al.   CORAL REEFS

Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission

(2015) Detmer Sipkema et al.   ENVIRONMENTAL MICROBIOLOGY

Whole Genome Sequencing of the SymbiontPseudovibriosp. from the Intertidal Marine SpongePolymastia penicillusRevealed a Gene Repertoire for Host-Switching Permissive Lifestyle

(2015) Anoop Alex et al.   Genome Biology and Evolution

Bacaryolanes A–C, Rare Bacterial Caryolanes from a Mangrove Endophyte

(2015) Ling Ding et al.   JOURNAL OF NATURAL PRODUCTS

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

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource

(2015) Jesse CJ van Dam et al.   Journal of Biomedical Semantics

Substrate Use of Pseudovibrio sp. Growing in Ultra-Oligotrophic Seawater

(2015) Anne Schwedt et al.   PLoS One

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Characterisation of Non-Autoinducing Tropodithietic Acid (TDA) Production from Marine Sponge Pseudovibrio Species

(2014) Catriona Harrington et al.   Marine Drugs

Marine Pseudovibrio sp. as a Novel Source of Antimicrobials

(2014) Susan Crowley et al.   Marine Drugs

Structure of a type IV secretion system

(2014) Harry H. Low et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

orthAgogue: an agile tool for the rapid prediction of orthology relations

(2013) O. K. Ekseth et al.   BIOINFORMATICS

The genusPseudovibriocontains metabolically versatile bacteria adapted for symbiosis

(2013) Vladimir Bondarev et al.   ENVIRONMENTAL MICROBIOLOGY

Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress

(2013) Lu Fan et al.   ISME Journal

Physiological characterization of aerobic culturable bacteria in the intestine of the sea cucumber Apostichopus japonicus

(2013) Xiaochi Zhang et al.   JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY

Characterization of Cultivable Bacteria from Brazilian Sponges

(2013) Juliana F. Santos-Gandelman et al.   MARINE BIOTECHNOLOGY

Subtilomycin: A New Lantibiotic from Bacillus subtilis Strain MMA7 Isolated from the Marine Sponge Haliclona simulans

(2013) Robert Phelan et al.   Marine Drugs

The Ammonia Oxidizing and Denitrifying Prokaryotes Associated with Sponges from Different Sea Areas

(2013) Minqi Han et al.   MICROBIAL ECOLOGY

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

(2013) Mary T. H. D. Nguyen et al.   MOLECULAR ECOLOGY

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

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Phylogenetically Diverse ureC Genes and Their Expression Suggest the Urea Utilization by Bacterial Symbionts in Marine Sponge Xestospongia testudinaria

(2013) Jing Su et al.   PLoS One

Antimicrobial Activity of Heterotrophic Bacterial Communities from the Marine Sponge Erylus discophorus (Astrophorida, Geodiidae)

(2013) Ana Patrícia Graça et al.   PLoS One

The Type VI secretion system – a widespread and versatile cell targeting system

(2013) Sarah J. Coulthurst   RESEARCH IN MICROBIOLOGY

Genome of the R-body producing marine alphaproteobacterium Labrenzia alexandrii type strain (DFL-11T)

(2013) Anne Fiebig et al.   Standards in Genomic Sciences

Bartonella entry mechanisms into mammalian host cells

(2012) Simone C. Eicher et al.   CELLULAR MICROBIOLOGY

Microbial Lifestyle and Genome Signatures

(2012)   CURRENT GENOMICS

Tetratricopeptide Repeat Motifs in the World of Bacterial Pathogens: Role in Virulence Mechanisms

(2012) Lukas Cerveny et al.   INFECTION AND IMMUNITY

Pseudovibrio axinellae sp. nov., isolated from an Irish marine sponge

(2012) J. A. O'Halloran et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A complex LuxR-LuxI type quorum sensing network in a roseobacterial marine sponge symbiont activates flagellar motility and inhibits biofilm formation

(2012) Jindong Zan et al.   MOLECULAR MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation of marine bacteria with antimicrobial activities from cultured and field-collected soft corals

(2012) Yu-Hsin Chen et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Exploration and Mining of the Bacterial Terpenome

(2011) David E. Cane et al.   ACCOUNTS OF CHEMICAL RESEARCH

Marine sponges and their microbial symbionts: love and other relationships

(2011) Nicole S. Webster et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and antimicrobial activity of Pseudovibrio spp. from Irish marine sponges

(2011) J.A. O’ Halloran et al.   JOURNAL OF APPLIED MICROBIOLOGY

Diversity and antimicrobial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp.

(2011) B. Flemer et al.   JOURNAL OF APPLIED MICROBIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica

(2010) Michael Yizhe Liu et al.   ISME Journal

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

(2010) Torsten Thomas et al.   ISME Journal

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Expression of Tropodithietic Acid Biosynthesis Is Controlled by a Novel Autoinducer

(2010) H. Geng et al.   JOURNAL OF BACTERIOLOGY

Bacteriocin as Weapons in the Marine Animal-Associated Bacteria Warfare: Inventory and Potential Applications as an Aquaculture Probiotic

(2010) Florie Desriac et al.   Marine Drugs

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

Isolation, characterization and phylogeny of sponge-associated bacteria with antimicrobial activities from Brazil

(2010) Olinda C.S. Santos et al.   RESEARCH IN MICROBIOLOGY

Phylogenetic diversity and antimicrobial activities of bryozoan-associated bacteria isolated from Mediterranean and Baltic Sea habitats

(2010) Herwig Heindl et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Nitrogen fixation and nitrogen transformations in marine symbioses

(2010) Cara L. Fiore et al.   TRENDS IN MICROBIOLOGY

Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences

Evidence for Vertical Transmission of Bacterial Symbionts from Adult to Embryo in the Caribbean Sponge Svenzea zeai

(2009) O. O. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mini-review: quorum sensing in the marine environment and its relationship to biofouling

(2009) Sergey Dobretsov et al.   BIOFOULING

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Microbial diversity associated with algae, ascidians and sponges from the north coast of São Paulo state, Brazil

(2009) Cláudia B.A. Menezes et al.   MICROBIOLOGICAL RESEARCH

The microbial ocean from genomes to biomes

(2009) Edward F. DeLong   NATURE

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Microbial Diversity Survey of Sponge Reproductive Stages and Mechanistic Insights into Vertical Transmission of Microbial Symbionts

(2008) S. Schmitt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil

(2008) Heather K Allen et al.   ISME Journal

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

(2008) Rebecca J Case et al.   ISME Journal

Roles of Coenzyme F420-Reducing Hydrogenases and Hydrogen- and F420-Dependent Methylenetetrahydromethanopterin Dehydrogenases in Reduction of F420 and Production of Hydrogen during Methanogenesis

(2008) E. L. Hendrickson et al.   JOURNAL OF BACTERIOLOGY

Characterization of the Microbial Community and Polyketide Biosynthetic Potential in the Palmerolide-Producing TunicateSynoicum adareanum

(2008) Christian S. Riesenfeld et al.   JOURNAL OF NATURAL PRODUCTS

Isolation and Analysis of Bacteria with Antimicrobial Activities from the Marine Sponge Haliclona simulans Collected from Irish Waters

(2008) Jonathan Kennedy et al.   MARINE BIOTECHNOLOGY