Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp.

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

(2015) Tracy D Ainsworth et al.   ISME Journal

Epitheliocystis in lake troutSalvelinus namaycush(Walbaum) is associated with a β-proteobacteria

(2015) E Contador et al.   JOURNAL OF FISH DISEASES

A new intracellular bacterium, Candidatus Similichlamydia labri sp. nov. (Chlamydiaceae) producing epitheliocysts in ballan wrasse, Labrus bergylta (Pisces, Labridae)

(2014) Andreas Steigen et al.   ARCHIVES OF MICROBIOLOGY

Characterization of ‘Candidatus Syngnamydia salmonis’ (Chlamydiales, Simkaniaceae), a bacterium associated with epitheliocystis in Atlantic salmon (Salmo salar L.)

(2014) Stian Nylund et al.   ARCHIVES OF MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Patterns of genome evolution that have accompanied host adaptation inSalmonella

(2014) Gemma C. Langridge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chlamydial infections of fish: Diverse pathogens and emerging causes of disease in aquaculture species

(2014) M.C. Stride et al.   VETERINARY MICROBIOLOGY

The Microbiome of the Red Sea Coral Stylophora pistillata Is Dominated by Tissue-Associated Endozoicomonas Bacteria

(2013) Till Bayer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular Characterization of "Candidatus Similichlamydia latridicola" gen. nov., sp. nov. (Chlamydiales: "Candidatus Parilichlamydiaceae"), a Novel Chlamydia-Like Epitheliocystis Agent in the Striped Trumpeter, Latris lineata (Forster)

(2013) M. C. Stride et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

A novel agent (Endozoicomonas elysicola) responsible for epitheliocystis in cobia Rachycentrum canadum larvae

(2013) M Mendoza et al.   DISEASES OF AQUATIC ORGANISMS

Amplicon pyrosequencing reveals spatial and temporal consistency in diazotroph assemblages of theAcropora milleporamicrobiome

(2013) Kimberley A. Lema et al.   ENVIRONMENTAL MICROBIOLOGY

Description of Endozoicomonas euniceicola sp. nov. and Endozoicomonas gorgoniicola sp. nov., bacteria isolated from the octocorals Eunicea fusca and Plexaura sp., and an emended description of the genus Endozoicomonas

(2013) R. E. Pike et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products

(2013) Sergey Nurk et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

‘Cand. Actinochlamydia clariae’ gen. nov., sp. nov., a Unique Intracellular Bacterium Causing Epitheliocystis in Catfish (Clarias gariepinus) in Uganda

(2013) Andreas Steigen et al.   PLoS One

Candidatus Syngnamydia Venezia, a Novel Member of the Phylum Chlamydiae from the Broad Nosed Pipefish, Syngnathus typhle

(2013) Alexander Fehr et al.   PLoS One

“Candidatus Similichlamydia laticola”, a Novel Chlamydia-like Agent of epitheliocystis in Seven Consecutive Cohorts of Farmed Australian Barramundi, Lates calcarifer (Bloch)

(2013) Megan C. Stride et al.   PLoS One

CGAL: computing genome assembly likelihoods

(2013) Atif Rahman et al.   GENOME BIOLOGY

Molecular Characterization of “Candidatus Parilichlamydia carangidicola,” a Novel Chlamydia-Like Epitheliocystis Agent in Yellowtail Kingfish, Seriola lalandi (Valenciennes), and the Proposal of a New Family, “Candidatus Parilichlamydiaceae” fam. nov. (Order Chlamydiales)

(2012) M. C. Stride et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

A Novel Betaproteobacterial Agent of Gill Epitheliocystis in Seawater Farmed Atlantic Salmon (Salmo salar)

(2012) Elena R. Toenshoff et al.   PLoS One

TrakEM2 Software for Neural Circuit Reconstruction

(2012) Albert Cardona et al.   PLoS One

A natural freshwater origin for two chlamydial species, Candidatus Piscichlamydia salmonis and Candidatus Clavochlamydia salmonicola, causing mixed infections in wild brown trout (Salmo trutta)

(2011) Heike Schmidt-Posthaus et al.   ENVIRONMENTAL MICROBIOLOGY

Permissivity of fish cell lines to threeChlamydia-related bacteria:Waddlia chondrophila,Estrella lausannensisandParachlamydia acanthamoebae

(2011) Carole Kebbi-Beghdadi et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Health of farmed fish: its relation to fish welfare and its utility as welfare indicator

(2011) Helmut Segner et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Development of a New Chlamydiales-Specific Real-Time PCR and Its Application to Respiratory Clinical Samples

(2011) Julia Lienard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Epitheliocystis in Atlantic salmon, Salmo salar L., farmed in fresh water in Ireland is associated with ‘Candidatus Clavochlamydia salmonicola’ infection

(2010) S O Mitchell et al.   JOURNAL OF FISH DISEASES

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Severe mortality in mesocosm-reared sharpsnout sea bream Diplodus puntazzo larvae due to epitheliocystis infection

(2008) P Katharios et al.   DISEASES OF AQUATIC ORGANISMS

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients

(2008) M. T. G. Holden et al.   JOURNAL OF BACTERIOLOGY

Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques

(2008) Rudolf Amann et al.   NATURE REVIEWS MICROBIOLOGY