Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera

Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera

(2023) Kshitij Tandon et al.   GigaScience

The evolution and role of eukaryotic-like domains in environmental intracellular bacteria: the battle with a eukaryotic cell

(2022) Jessica E Martyn et al.   FEMS MICROBIOLOGY REVIEWS

The role of the endolithic alga Ostreobium spp. during coral bleaching recovery

(2022) Claudia Tatiana Galindo-Martínez et al.   Scientific Reports

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

(2022) Zhichao Zhou et al.   Microbiome

Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle

(2022) Claudia Pogoreutz et al.   ISME Journal

Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business

(2022) Kshitij Tandon et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses

(2022) Francesco Ricci et al.   mSystems

DMSP Production by Coral-Associated Bacteria

(2022) Felicity W.I. Kuek et al.   Frontiers in Marine Science

Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility

(2022) Anny Cárdenas et al.   ISME Journal

Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes

(2022) Kshitij Tandon et al.   mSystems

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

(2022) Jie Li et al.   mSystems

A genomic view of the microbiome of coral reef demosponges

(2021) S. J. Robbins et al.   ISME Journal

Multiple techniques point to oxygenic phototrophs dominating the Isopora palifera skeletal microbiome

(2021) Francesco Ricci et al.   CORAL REEFS

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

(2021) Talisa Doering et al.   Microbiome

Microbially facilitated nitrogen cycling in tropical corals

(2021) Thomas D. Glaze et al.   ISME Journal

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

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

Coral Probiotics: Premise, Promise, Prospects

(2020) Raquel S. Peixoto et al.   Annual Review of Animal Biosciences

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

Coral microbiome dynamics, functions and design in a changing world

(2019) Madeleine J. H. van Oppen et al.   NATURE REVIEWS MICROBIOLOGY

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

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Metagenome of Acropora palmata coral rubble: Potential metabolic pathways and diversity in the reef ecosystem

(2019) Andrés Sánchez-Quinto et al.   PLoS One

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

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

Bacteria are important dimethylsulfoniopropionate producers in coastal sediments

(2019) Beth T. Williams et al.   Nature Microbiology

Biodiversity of endolithic fungi in coral skeletons and other reef substrates revealed with 18S rDNA metabarcoding

(2019) Aristóteles Góes-Neto et al.   CORAL REEFS

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health

(2019) Mathieu Pernice et al.   ISME Journal

Beneath the surface: community assembly and functions of the coral skeleton microbiome

(2019) Francesco Ricci et al.   Microbiome

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation

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

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

(2018) Chirag Jain 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

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Highly structured prokaryote communities exist within the skeleton of coral colonies

(2017) Vanessa R Marcelino et al.   ISME Journal

Defining the Core Microbiome in Corals’ Microbial Soup

(2017) Alejandra Hernandez-Agreda et al.   TRENDS IN MICROBIOLOGY

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience

(2017) Raquel S. Peixoto et al.   Frontiers in Microbiology

13 C and 15 N assimilation and organic matter translocation by the endolithic community in the massive coral Porites lutea

(2017) Laddawan Sangsawang et al.   Royal Society Open Science

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont

(2017) Lin Cai et al.   Scientific Reports

Prokaryotic and Highly-Repetitive WD40 Proteins: A Systematic Study

(2017) Xue-Jia Hu et al.   Scientific Reports

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

(2016) P. R. Frade et al.   Environmental Chemistry

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

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Evolution and function of eukaryotic-like proteins from sponge symbionts

(2016) David Reynolds et al.   MOLECULAR ECOLOGY

Reefgenomics.Org - a repository for marine genomics data

(2016) Yi Jin Liew et al.   Database-The Journal of Biological Databases and Curation

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae

(2016) Vanessa Rossetto Marcelino et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu 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

The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts

(2015) Tracy D Ainsworth et al.   ISME Journal

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

Nitrogen cycling in corals: the key to understanding holobiont functioning?

(2015) Nils Rädecker et al.   TRENDS IN MICROBIOLOGY

Tandem-repeat protein domains across the tree of life

(2015) Kristin K. Jernigan et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

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

Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coralAcropora millepora

(2014) Kimberley A. Lema et al.   MOLECULAR ECOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Ankyrin domains across the Tree of Life

(2014) Kristin K. Jernigan et al.   PeerJ

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

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

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

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

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

(2012) Lukas Cerveny et al.   INFECTION AND IMMUNITY

Geographic Specific Coral-Associated Ammonia-Oxidizing Archaea in the Northern Gulf of Eilat (Red Sea)

(2012) Nachshon Siboni et al.   MICROBIAL ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Bacterial assemblages differ between compartments within the coral holobiont

(2010) M. J. Sweet et al.   CORAL REEFS

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

(2010) Torsten Thomas et al.   ISME Journal

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Microbial functional structure ofMontastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies

(2009) Nikole E. Kimes et al.   ENVIRONMENTAL MICROBIOLOGY

Diazotrophic bacteria associated with Hawaiian Montipora corals: Diversity and abundance in correlation with symbiotic dinoflagellates

(2009) N.D. Olson et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Chlamydiae as Symbionts in Eukaryotes

(2008) Matthias Horn   Annual Review of Microbiology

Global distribution and diversity of coral-associatedArchaeaand their possible role in the coral holobiont nitrogen cycle

(2008) Nachshon Siboni et al.   ENVIRONMENTAL MICROBIOLOGY

IMAGING OF OXYGEN DYNAMICS WITHIN THE ENDOLITHIC ALGAL COMMUNITY OF THE MASSIVE CORALPORITES LOBATA

(2008) Michael Kühl et al.   JOURNAL OF PHYCOLOGY