Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera

(2019) Shan-Hua Yang et al.   Microbiome

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Soft corals are significant DMSP producers in tropical and temperate reefs

(2018) Trent D. Haydon et al.   MARINE BIOLOGY

Type IV secretion in Gram-negative and Gram-positive bacteria

(2018) Elisabeth Grohmann et al.   MOLECULAR MICROBIOLOGY

Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts

(2018) Todd C. LaJeunesse et al.   CURRENT BIOLOGY

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

(2018) F. Joseph Pollock et al.   Nature Communications

Elevated CO2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp.

(2018) Paul A. O’Brien et al.   Frontiers in Microbiology

Endozoicomonas acroporae sp. nov., isolated from Acropora coral

(2017) Shih-Yi Sheu et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Dynamics of coral-associated bacterial communities acclimated to temperature stress based on recent thermal history

(2017) Jia-Ho Shiu et al.   Scientific Reports

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals

(2017) Shan-Hua Yang et al.   Frontiers in Microbiology

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

(2017) Matthew J. Neave et al.   Scientific Reports

Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems

(2016) David G. Bourne et al.   Annual Review of Microbiology

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

(2016) Matthew J. Neave et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales

(2016) Matthew J Neave et al.   ISME Journal

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

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

Prevalence of potential nitrogen-fixing, green sulfur bacteria in the skeleton of reef-building coralIsopora palifera

(2016) Shan-Hua Yang et al.   LIMNOLOGY AND OCEANOGRAPHY

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea

(2016) Maren Ziegler et al.   MARINE POLLUTION BULLETIN

Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria

(2016) Jeroen A. J. M. van de Water et al.   MICROBIAL ECOLOGY

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales

(2016) Jesse R. Zaneveld et al.   Nature Communications

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

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

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

EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

(2015) Valerie Eichinger et al.   NUCLEIC ACIDS RESEARCH

Identification of the algal dimethyl sulfide-releasing enzyme: A missing link in the marine sulfur cycle

(2015) U. Alcolombri et al.   SCIENCE

DddD Is a CoA-Transferase/Lyase Producing Dimethyl Sulfide in the Marine Environment

(2014) Uria Alcolombri et al.   BIOCHEMISTRY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age

(2014) Jan P. Meier-Kolthoff et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Effects of environmental factors on dimethylated sulfur compounds and their potential role in the antioxidant system of the coral holobiont

(2014) E. S. M. Deschaseaux et al.   LIMNOLOGY AND OCEANOGRAPHY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals

(2013) Melissa Garren et al.   ISME Journal

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

DMSP biosynthesis by an animal and its role in coral thermal stress response

(2013) Jean-Baptiste Raina et al.   NATURE

16SrDNA Pyrosequencing of the Mediterranean Gorgonian Paramuricea clavata Reveals a Link among Alterations in Bacterial Holobiont Members, Anthropogenic Influence and Disease Outbreaks

(2013) Luigi Vezzulli et al.   PLoS One

Heat-Stress and Light-Stress Induce Different Cellular Pathologies in the Symbiotic Dinoflagellate during Coral Bleaching

(2013) C. A. Downs et al.   PLoS One

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

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

Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes

(2011) Andrew R. J. Curson et al.   NATURE REVIEWS MICROBIOLOGY

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Bacterial Catabolism of Dimethylsulfoniopropionate (DMSP)

(2011) Chris R. Reisch et al.   Frontiers in Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Do the organic sulfur compounds DMSP and DMS drive coral microbial associations?

(2010) Jean-Baptiste Raina et al.   TRENDS IN MICROBIOLOGY

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

(2009) J.-B. Raina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular dissection of bacterial acrylate catabolism - unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production

(2009) Jonathan D. Todd et al.   ENVIRONMENTAL MICROBIOLOGY

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine α-proteobacteria and Rhodobacter sphaeroides

(2008) A. R. J. Curson et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses

(2008) A. W. B. Johnston et al.   JOURNAL OF EXPERIMENTAL BOTANY