Phylogeny and genomics of SAUL, an enigmatic bacterial lineage frequently associated with marine sponges

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

(2017) Beate M Slaby et al.   ISME Journal

Marine natural products

(2017) John W. Blunt et al.   NATURAL PRODUCT REPORTS

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges

(2017) Gerald Lackner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the HMA-LMA Status in Marine Sponges by Machine Learning

(2017) Lucas Moitinho-Silva et al.   Frontiers in Microbiology

Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

(2017) Ren-Mao Tian et al.   mSystems

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

Restructuring of the sponge microbiome favors tolerance to ocean acidification

(2016) M. Ribes et al.   Environmental Microbiology Reports

The Sponge Hologenome

(2016) Nicole S. Webster et al.   mBio

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

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

(2016) Hannes Horn et al.   Frontiers in Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

The HMA-LMA Dichotomy Revisited: an Electron Microscopical Survey of 56 Sponge Species

(2016) Volker Gloeckner et al.   BIOLOGICAL BULLETIN

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

Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms

(2015) Laura V. Flórez et al.   NATURAL PRODUCT REPORTS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

(2015) Fan Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

(2015) Ilia Burgsdorf et al.   mBio

HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes

(2015) Marcus Nguyen et al.   Toxins

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)

(2015) Noha H. Youssef et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

(2014) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

Polyketide Synthases in the Microbiome of the Marine Sponge Plakortis halichondrioides: A Metagenomic Update

(2014) Gerardo Della Sala et al.   Marine Drugs

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny, Cell-Compartmentation, Eukaryote-Like Repeat Proteins, and Other Genomic Features

(2014) Janine Kamke et al.   PLoS One

Symbiotic Adaptation Drives Genome Streamlining of the Cyanobacterial Sponge Symbiont "Candidatus Synechococcus spongiarum"

(2014) Z.-M. Gao et al.   mBio

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Temporal molecular and isotopic analysis of active bacterial communities in two New Zealand sponges

(2013) Rachel Simister et al.   FEMS MICROBIOLOGY ECOLOGY

Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress

(2013) Lu Fan et al.   ISME Journal

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

(2013) Janine Kamke et al.   ISME Journal

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

(2013) K. Vasu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

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

(2012) Lukas Cerveny et al.   INFECTION AND IMMUNITY

‘Sponge-specific’ bacteria are widespread (but rare) in diverse marine environments

(2012) Michael W Taylor et al.   ISME Journal

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

Natural Products As Sources of New Drugs over the 30 Years from 1981 to 2010

(2012) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Ectyoplasia ferox, an Experimentally Tractable Model for Vertical Microbial Transmission in Marine Sponges

(2012) Volker Gloeckner et al.   MICROBIAL ECOLOGY

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

Thermal and Sedimentation Stress Are Unlikely Causes of Brown Spot Syndrome in the Coral Reef Sponge, Ianthella basta

(2012) Heidi M. Luter et al.   PLoS One

Sponge-Microbe Associations Survive High Nutrients and Temperatures

(2012) Rachel Simister 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

Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

(2011) Naomi F. Montalvo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Chemical Ecology of Sponges on Caribbean Reefs: Natural Products Shape Natural Systems

(2011) Joseph R. Pawlik   BIOSCIENCE

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

(2011) Rachel L. Simister et al.   ENVIRONMENTAL MICROBIOLOGY

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Evolution and classification of the CRISPR–Cas systems

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

The larval sponge holobiont exhibits high thermal tolerance

(2011) Nicole S. Webster et al.   Environmental Microbiology Reports

CRISPR/Cas System and Its Role in Phage-Bacteria Interactions

(2010) Hélène Deveau et al.   Annual Review of Microbiology

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

Activity profiles for marine sponge-associated bacteria obtained by 16S rRNA vs 16S rRNA gene comparisons

(2010) Janine Kamke 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

Functional diversity of ankyrin repeats in microbial proteins

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

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Role for the Ankyrin eukaryotic-like genes of Legionella pneumophila in parasitism of protozoan hosts and human macrophages

(2008) Fabien Habyarimana et al.   ENVIRONMENTAL MICROBIOLOGY

The functional roles of marine sponges

(2008) James J. Bell   ESTUARINE COASTAL AND SHELF SCIENCE

Phototrophic nutrition and symbiont diversity of two Caribbean sponge–cyanobacteria symbioses

(2008) PM Erwin et al.   MARINE ECOLOGY PROGRESS SERIES

Bleaching and stress in coral reef ecosystems:hsp70expression by the giant barrel spongeXestospongia muta

(2008) SUSANNA LÓPEZ-LEGENTIL et al.   MOLECULAR ECOLOGY

Metabolites from symbiotic bacteria

(2008) Jörn Piel   NATURAL PRODUCT REPORTS

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

(2008) I. Grissa et al.   NUCLEIC ACIDS RESEARCH