Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis

Comparing the Role of ROS and RNS in the Thermal Stress Response of Two Cnidarian Models, Exaiptasia diaphana and Galaxea fascicularis

(2023) Talisa Doering et al.   Antioxidants

Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease

(2023) Blake Ushijima et al.   Communications Biology

Advancing coral microbiome manipulation to build long-term climate resilience

(2023) Talisa Doering et al.   Microbiology Australia

Exploring microbiome engineering as a strategy for improved thermal tolerance in Exaiptasia diaphana

(2022) Ashley M. Dungan et al.   JOURNAL OF APPLIED MICROBIOLOGY

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

(2022) Zhichao Zhou et al.   Microbiome

Lack of evidence for the oxidative stress theory of bleaching in the sea anemone, Exaiptasia diaphana, under elevated temperature

(2022) Ashley M. Dungan et al.   CORAL REEFS

Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater

(2022) Jingli Liu et al.   Microbiome

High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata

(2022) Naohisa Wada et al.   Science Advances

Cultured Bacteria Provide Insight into the Functional Potential of the Coral-Associated Microbiome

(2022) Jie Li et al.   mSystems

Heat stress destabilizes symbiotic nutrient cycling in corals

(2021) Nils Rädecker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs

(2021) Justin Maire et al.   ISME Journal

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues

(2021) Talisa Doering et al.   Microbiome

A role for bacterial experimental evolution in coral bleaching mitigation?

(2021) Justin Maire et al.   TRENDS IN MICROBIOLOGY

Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality

(2021) Erika P. Santoro et al.   Science Advances

Insights into the Cultured Bacterial Fraction of Corals

(2021) Michael Sweet et al.   mSystems

Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians

(2021) Ashley M. Dungan et al.   Microbial Biotechnology

Emergent properties in the responses of tropical corals to recurrent climate extremes

(2021) Terry P. Hughes et al.   CURRENT BIOLOGY

Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks

(2020) Jennifer L. Matthews et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2020) Kshitij Tandon et al.   ISME Journal

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transporters of glucose and other carbohydrates in bacteria

(2020) Jean-Marc Jeckelmann et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Dimethylsulfoniopropionate Sulfur and Methyl Carbon Assimilation in Ruegeria Species

(2020) Joseph S. Wirth et al.   mBio

Relative stability of the Pocillopora acuta microbiome throughout a thermal stress event

(2019) Hannah E. Epstein et al.   CORAL REEFS

Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea

(2019) Katarina Damjanovic et al.   Frontiers in Microbiology

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

(2019) Steven J. Robbins et al.   Nature Microbiology

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

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Exploring coral microbiome assemblages in the South China Sea

(2018) Lin Cai et al.   Scientific Reports

New Insight Into the Diversity of SemiSWEET Sugar Transporters and the Homologs in Prokaryotes

(2018) Baolei Jia et al.   Frontiers in Genetics

Metabolic specialization of denitrifiers in permeable sediments controls N2 O emissions

(2018) Hannah K. Marchant et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host

(2018) Lauren Speare et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes

(2018) Megan J. Huggett et al.   Environmental Microbiology Reports

Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation

(2018) Phillipe M. Rosado et al.   ISME Journal

Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

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

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

A denitrifying community associated with a major, marine nitrogen fixer

(2017) Christopher J. Coates et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial community dynamics are linked to patterns of coral heat tolerance

(2017) Maren Ziegler et al.   Nature Communications

Microbiome engineering: Current applications and its future

(2017) Jee Loon Foo et al.   Biotechnology Journal

The Type VI Secretion System: A Dynamic System for Bacterial Communication?

(2017) Mathias Gallique et al.   Frontiers in Microbiology

Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process

(2017) Andrew R. J. Curson et al.   Nature Microbiology

The contribution of microbial biotechnology to mitigating coral reef degradation

(2017) Katarina Damjanovic et al.   Microbial Biotechnology

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

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

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

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

SalmonellaTyphimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut

(2016) Thibault G. Sana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Alkyl hydroperoxide reductase fromBacillus aquimarisMKSC 6.2 protectsEsherichia colifrom oxidative stress

(2015) Dessy Natalia et al.   JOURNAL OF BASIC MICROBIOLOGY

Coral-the world's most diverse symbiotic ecosystem

(2015) Linda L. Blackall et al.   MOLECULAR ECOLOGY

Building coral reef resilience through assisted evolution

(2015) Madeleine J. H. van Oppen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of the Roseovarius mucosus type strain (DSM 17069T), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii

(2015) Thomas Riedel et al.   Standards in Genomic Sciences

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Differential nitric oxide synthesis and host apoptotic events correlate with bleaching susceptibility in reef corals

(2014) T. D. Hawkins et al.   CORAL REEFS

Cryptic carbon and sulfur cycling between surface ocean plankton

(2014) Bryndan P. Durham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential Role of Carotenoids as Antioxidants in Human Health and Disease

(2014) Joanna Fiedor et al.   Nutrients

Zeaxanthin Production by Novel Marine Isolates from Coastal sand of India and its Antioxidant Properties

(2013) Sudharshan Prabhu et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Nitric oxide mediates coral bleaching through an apoptotic-like cell death pathway: evidence from a model sea anemone-dinoflagellate symbiosis

(2013) Thomas D. Hawkins et al.   FASEB JOURNAL

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

(2013) Melissa Garren et al.   ISME Journal

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Highly Heterogeneous Bacterial Communities Associated with the South China Sea Reef Corals Porites lutea, Galaxea fascicularis and Acropora millepora

(2013) Jie Li et al.   PLoS One

Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea

(2012) Angela D. Hatton et al.   BIOGEOCHEMISTRY

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

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

Evidence that glucose is the major transferred metabolite in dinoflagellate-cnidarian symbiosis

(2012) M. S. Burriesci et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Nitric Oxide Production and Tolerance Differ Among Symbiodinium Types Exposed to Heat Stress

(2012) T. D. Hawkins et al.   PLANT AND CELL PHYSIOLOGY

Nutrient enrichment can increase the susceptibility of reef corals to bleaching

(2012) Jörg Wiedenmann et al.   Nature Climate Change

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

A new conceptual model for the warm-water breakdown of the coral–algae endosymbiosis

(2009) Scott A. Wooldridge   MARINE AND FRESHWATER RESEARCH

Functional diversity of ankyrin repeats in microbial proteins

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

Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis

(2008) V. M. Weis   JOURNAL OF EXPERIMENTAL BIOLOGY

Heat Stress Stimulates Nitric Oxide Production in Symbiodinium microadriaticum: A Possible Linkage between Nitric Oxide and the Coral Bleaching Phenomenon

(2008) J. N. Bouchard et al.   PLANT AND CELL PHYSIOLOGY