Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts

Single-bacterial genomics validates rich and varied specialized metabolism of uncultivatedEntotheonellasponge symbionts

(2018) Tetsushi Mori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes

(2018) Tory A. Hendry et al.   mBio

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

(2018) Chirag Jain et al.   Nature Communications

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

(2017) Beate M Slaby et al.   ISME Journal

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

(2017) Lucas Moitinho-Silva et al.   ISME Journal

Expression of eukaryotic-like protein in the microbiome of sponges

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

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

Short-chain alkanes fuel mussel and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps

(2017) Maxim Rubin-Blum et al.   Nature 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

Hologenome analysis of two marine sponges with different microbiomes

(2016) Taewoo Ryu et al.   BMC GENOMICS

Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis

(2016) Ruby Ponnudurai et al.   ISME Journal

Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase

(2016) Bram Vekeman et al.   MICROBIAL ECOLOGY

The Sponge Hologenome

(2016) Nicole S. Webster et al.   mBio

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges

(2016) Jon T. Hestetun et al.   Frontiers in Microbiology

Improved ultrastructure of marine invertebrates using non-toxic buffers

(2016) Jacqueline Montanaro et al.   PeerJ

Origins and Evolutionary Flexibility of Chemosynthetic Symbionts From Deep-Sea Animals

(2016) Jillian M. Petersen et al.   BIOLOGICAL BULLETIN

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

(2016) Volker Gloeckner et al.   BIOLOGICAL BULLETIN

Endosymbiont evolution: predictions from theory and surprises from genomes

(2015) Jennifer J. Wernegreen   Annals of the New York Academy of Sciences

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

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

An out-of-body experience: the extracellular dimension for the transmission of mutualistic bacteria in insects

(2015) H. Salem et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

gbtools: Interactive Visualization of Metagenome Bins in R

(2015) Brandon K. B. Seah et al.   Frontiers in Microbiology

The Tiniest Tiny Genomes

(2014) Nancy A. Moran et al.   Annual Review of Microbiology

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics

(2014) Lucas Moitinho-Silva et al.   ENVIRONMENTAL MICROBIOLOGY

Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis

(2014) Kelly F. Oakeson et al.   Genome Biology and Evolution

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Reductive genome evolution at both ends of the bacterial population size spectrum

(2014) Bérénice Batut et al.   NATURE REVIEWS MICROBIOLOGY

Cooperation, communication, and co-evolution: grand challenges in microbial symbiosis research

(2014) Nicole S. Webster   Frontiers in Microbiology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Microbial Communities of Deep-Sea Methane Seeps at Hikurangi Continental Margin (New Zealand)

(2013) S. Emil Ruff et al.   PLoS One

Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts

(2013) M. Kleiner et al.   mBio

Highly efficient methane biocatalysis revealed in a methanotrophic bacterium

(2013) M. G. Kalyuzhnaya et al.   Nature Communications

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

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

(2012) Y. Peng et al.   BIOINFORMATICS

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

(2012) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

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

Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations

(2012) Shawn M. Arellano et al.   MICROBIAL ECOLOGY

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

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

Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use

(2012) M. Kleiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Microbial diversity in Frenulata (Siboglinidae, Polychaeta) species from mud volcanoes in the Gulf of Cadiz (NE Atlantic)

(2011) Clara F. Rodrigues et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Susanne Schmitt et al.   ISME Journal

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Symbiont–host relationships in chemosynthetic mussels: A comprehensive lipid biomarker study

(2011) Matthias Y. Kellermann et al.   ORGANIC GEOCHEMISTRY

Toxin–antitoxin systems: why so many, what for?

(2010) Laurence Van Melderen   CURRENT OPINION IN MICROBIOLOGY

Association of Thioautotrophic Bacteria with Deep-Sea Sponges

(2010) Miyuki Nishijima et al.   MARINE BIOTECHNOLOGY

Diversity and Function of Epibiotic Microbial Communities on the Galatheid Crab, Shinkaia crosnieri

(2010) Tomo-o Watsuji et al.   MICROBES AND ENVIRONMENTS

Bacterial genomic G+C composition-eliciting environmental adaptation

(2009) Scott Mann et al.   GENOMICS

Origin, distribution, and alteration of asphalts at Chapopote Knoll, Southern Gulf of Mexico

(2009) Markus Brüning et al.   MARINE AND PETROLEUM GEOLOGY

Methanotrophic symbioses in marine invertebrates

(2009) Jillian M. Petersen et al.   Environmental Microbiology Reports

Unexpected co-occurrence of six bacterial symbionts in the gills of the cold seep mussel Idas sp. (Bivalvia: Mytilidae)

(2008) Sébastien Duperron et al.   ENVIRONMENTAL MICROBIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY