Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade

A test of the sponge-loop hypothesis for emergent Caribbean reef sponges

(2018) SE McMurray et al.   MARINE ECOLOGY PROGRESS SERIES

Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes

(2018) Cintia P. J. Rua et al.   MICROBIAL ECOLOGY

A test of the sponge-loop hypothesis for emergent Caribbean reef sponges

(2018) SE McMurray et al.   MARINE ECOLOGY PROGRESS SERIES

The sponge holobiont in a changing ocean: from microbes to ecosystems

(2018) L. Pita et al.   Microbiome

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

(2017) Carmen Astudillo-García et al.   ENVIRONMENTAL MICROBIOLOGY

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

(2017) Maliheh Mehrshad et al.   ISME Journal

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

(2017) Beate M Slaby et al.   ISME Journal

Consumption of dissolved organic carbon by Caribbean reef sponges

(2017) Daniel R. Hoer et al.   LIMNOLOGY AND OCEANOGRAPHY

Expression of eukaryotic-like protein in the microbiome of sponges

(2017) C. Díez-Vives et al.   MOLECULAR ECOLOGY

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

Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico “Dead Zone”

(2017) J. Cameron Thrash et al.   mBio

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

(2017) Zachary Landry et al.   mBio

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

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

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution and function of eukaryotic-like proteins from sponge symbionts

(2016) David Reynolds et al.   MOLECULAR ECOLOGY

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

Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

(2016) Martin T. Jahn et al.   Scientific Reports

Review of human hand microbiome research

(2015) Sarah L. Edmonds-Wilson et al.   JOURNAL OF DERMATOLOGICAL SCIENCE

Sponge waste that fuels marine oligotrophic food webs: a re-assessment of its origin and nature

(2015) Manuel Maldonado   Marine Ecology-An Evolutionary Perspective

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

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian

(2015) Zongjun Yin 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

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange

(2015) Cara L. Fiore et al.   Frontiers in Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Diversity and genomic insights into the unculturedChloroflexifrom the human microbiota

(2014) Alisha G. Campbell et al.   ENVIRONMENTAL MICROBIOLOGY

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

(2014) Kristina Bayer et al.   FEMS MICROBIOLOGY ECOLOGY

Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR

(2014) Kristina Bayer et al.   FEMS MICROBIOLOGY ECOLOGY

Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria

(2014) C. E. King et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

(2013) Janine Kamke et al.   ISME Journal

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

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

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.

(2012) Radhey S. Gupta et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Functional convergence of microbes associated with temperate marine sponges

(2012) M. Ribes et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2012) Lukas Cerveny et al.   INFECTION AND IMMUNITY

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

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

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

Genomic Mining for Novel FADH2-Dependent Halogenases in Marine Sponge-Associated Microbial Consortia

(2012) Kristina Bayer et al.   MARINE BIOTECHNOLOGY

Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

(2012) Sheila Marie Pimentel-Elardo et al.   Marine Drugs

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

Global Diversity of Sponges (Porifera)

(2012) Rob W. M. Van Soest 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

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

(2011) Joseph R. Pawlik   BIOSCIENCE

Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Torsten Thomas et al.   ISME Journal

Bacterial polymers: biosynthesis, modifications and applications

(2010) Bernd H. A. Rehm   NATURE REVIEWS MICROBIOLOGY

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

(2010) A. C. Y. Ng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cultivation of Uncultured Chloroflexi Subphyla: Significance and Ecophysiology of Formerly Uncultured Chloroflexi 'Subphylum I' with Natural and Biotechnological Relevance

(2009) Takeshi Yamada et al.   MICROBES AND ENVIRONMENTS

Strategies for acquiring the phospholipid metabolite inositol in pathogenic bacteria, fungi and protozoa: making it and taking it

(2009) T. B. Reynolds   MICROBIOLOGY-SGM

PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification

(2009) Alexander Siegl et al.   Environmental Microbiology Reports

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic

(2008) Marta M. Varela et al.   ENVIRONMENTAL MICROBIOLOGY

The functional roles of marine sponges

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

Oxygen dynamics and transport in the Mediterranean sponge Aplysina aerophoba

(2008) Friederike Hoffmann et al.   MARINE BIOLOGY