Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

(2016) Leighton Pritchard et al.   Analytical Methods

The deep-sea glass sponge L ophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur

(2016) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolution and function of eukaryotic-like proteins from sponge symbionts

(2016) David Reynolds et al.   MOLECULAR ECOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

(2016) David Burstein et al.   Nature Communications

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

(2016) Stefano Romano et al.   Frontiers in Microbiology

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes

(2016) Hannes Horn et al.   Frontiers in Microbiology

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals

(2016) Jean-Baptiste Raina et al.   PeerJ

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

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

Pseudomonas syringae pv. tomato DC3000 Type III Secretion Effector Polymutants Reveal an Interplay between HopAD1 and AvrPtoB

(2015) Hai-Lei Wei et al.   Cell Host & Microbe

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

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

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

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.

(2015) Bhavjinder K. Dhillon et al.   NUCLEIC ACIDS RESEARCH

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

(2015) Ilia Burgsdorf et al.   mBio

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

(2015) William C. Nelson et al.   Frontiers in Microbiology

Tandem-repeat protein domains across the tree of life

(2015) Kristin K. Jernigan et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Marine Pseudovibrio sp. as a Novel Source of Antimicrobials

(2014) Susan Crowley et al.   Marine Drugs

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

(2014) Pedro H. Oliveira et al.   NUCLEIC ACIDS RESEARCH

Diversification of bacterial genome content through distinct mechanisms over different timescales

(2014) Nicholas J. Croucher et al.   Nature Communications

Ankyrin domains across the Tree of Life

(2014) Kristin K. Jernigan et al.   PeerJ

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

(2013) Bruno Contreras-Moreira et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the north-east Atlantic

(2013) Ana I.S. Esteves et al.   FEMS MICROBIOLOGY ECOLOGY

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

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

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Ana Patrícia Graça et al.   PLoS One

Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)

(2013) Anoop Alex et al.   PLoS One

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

Pseudomonas syringae naturally lacking the canonical type III secretion system are ubiquitous in nonagricultural habitats, are phylogenetically diverse and can be pathogenic

(2012) Moudjahidou Demba Diallo et al.   ISME Journal

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

The evolution of metazoan extracellular matrix

(2012) Richard O. Hynes   JOURNAL OF CELL BIOLOGY

Protein Export According to Schedule: Architecture, Assembly, and Regulation of Type III Secretion Systems from Plant- and Animal-Pathogenic Bacteria

(2012) D. Buttner   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

High-Density Transcriptional Initiation Signals Underline Genomic Islands in Bacteria

(2012) Qianli Huang et al.   PLoS One

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

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

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

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

α-N-Acetylgalactosaminidase from Infant-associated Bifidobacteria Belonging to Novel Glycoside Hydrolase Family 129 Is Implicated in Alternative Mucin Degradation Pathway

(2011) Masashi Kiyohara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of the Antibacterial Compound Produced by the Marine Epiphytic Bacterium Pseudovibrio sp. D323 and Related Sponge-Associated Bacteria

(2011) Anahit Penesyan et al.   Marine Drugs

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

RNA remodeling and gene regulation by cold shock proteins

(2011) Sangita Phadtare et al.   RNA Biology

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

LRRfinder: A web application for the identification of leucine-rich repeats and an integrative Toll-like receptor database

(2010) V. Offord et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

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

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

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

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

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Standard operating procedure for computing pangenome trees

(2010) Lars Snipen et al.   Standards in Genomic Sciences

Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology

(2009) Tsai-Tien Tseng et al.   BMC MICROBIOLOGY

Synergistic role of curli and cellulose in cell adherence and biofilm formation of attaching and effacingEscherichia coliand identification of Fis as a negative regulator of curli

(2009) Zeus Saldaña et al.   ENVIRONMENTAL MICROBIOLOGY

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation

(2009) Michelle A Allen et al.   ISME Journal

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Majority of the Type III Effector Inventory ofPseudomonas syringaepv.tomatoDC3000 Can Suppress Plant Immunity

(2009) Ming Guo et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The Association of Virulence Factors with Genomic Islands

(2009) Shannan J. Ho Sui et al.   PLoS One

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES

Functional diversity of ankyrin repeats in microbial proteins

(2009) Souhaila Al-Khodor et al.   TRENDS IN MICROBIOLOGY

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes

(2009) Diego Cortez et al.   GENOME BIOLOGY

Evaluation of genomic island predictors using a comparative genomics approach

(2008) Morgan GI Langille et al.   BMC BIOINFORMATICS

Naturally Occurring Nonpathogenic Isolates of the Plant Pathogen Pseudomonas syringae Lack a Type III Secretion System and Effector Gene Orthologues

(2008) T. J. Mohr et al.   JOURNAL OF BACTERIOLOGY

Learning how to live together: genomic insights into prokaryote–animal symbioses

(2008) Andrés Moya et al.   NATURE REVIEWS GENETICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment

(2008) Torsten Thomas et al.   PLoS One