Characterization of a sponge microbiome using an integrative genome-centric approach

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

(2019) Florian U. Moeller et al.   ENVIRONMENTAL MICROBIOLOGY

Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge

(2018) Michelle Achlatis et al.   ISME Journal

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

(2018) Joel A Boyd et al.   NUCLEIC ACIDS RESEARCH

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

(2018) L. Pita et al.   Microbiome

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

Sponges to Be Winners under Near-Future Climate Scenarios

(2018) James J Bell et al.   BIOSCIENCE

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles

(2018) Sheila Podell et al.   ISME Journal

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

(2018) Kristina Bayer et al.   mSystems

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

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

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

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

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

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium

(2017) Elham Karimi et al.   Frontiers in Microbiology

Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV

(2017) Sepehr S. Mohammadi et al.   Frontiers in Microbiology

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

(2017) Elaina D. Graham et al.   PeerJ

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

(2016) Marc Sturm et al.   BMC BIOINFORMATICS

The deep-sea glass sponge L ophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur

(2016) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

Interactive effects of temperature and p CO2 on sponges: from the cradle to the grave

(2016) Holly M. Bennett et al.   GLOBAL CHANGE BIOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

The Sponge Hologenome

(2016) Nicole S. Webster et al.   mBio

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

Secretion systems in Gram-negative bacteria: structural and mechanistic insights

(2015) Tiago R. D. Costa et al.   NATURE REVIEWS MICROBIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

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

Riboflavin Provisioning Underlies Wolbachia's Fitness Contribution to Its Insect Host

(2015) M. Moriyama 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

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

(2015) Dongwan D. Kang et al.   PeerJ

Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics

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

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

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

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

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

Ankyrin domains across the Tree of Life

(2014) Kristin K. Jernigan et al.   PeerJ

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

The genusPseudovibriocontains metabolically versatile bacteria adapted for symbiosis

(2013) Vladimir Bondarev et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the north-east Atlantic

(2013) Ana I.S. Esteves et al.   FEMS MICROBIOLOGY ECOLOGY

Deep-sea sponge grounds enhance diversity and abundance of epibenthic megafauna in the Northwest Atlantic

(2013) Lindsay I. Beazley et al.   ICES JOURNAL OF MARINE SCIENCE

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

(2013) Janine Kamke et al.   ISME Journal

The Ammonia Oxidizing and Denitrifying Prokaryotes Associated with Sponges from Different Sea Areas

(2013) Minqi Han et al.   MICROBIAL ECOLOGY

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

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

Nitrogen Biogeochemistry in the Caribbean Sponge, Xestospongia muta: A Source or Sink of Dissolved Inorganic Nitrogen?

(2013) Cara L. Fiore et al.   PLoS One

Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs

(2013) Jasper M. de Goeij et al.   SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

‘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

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

A specific mix of generalists: bacterial symbionts in Mediterranean Ircinia spp.

(2011) Patrick M. Erwin et al.   FEMS MICROBIOLOGY ECOLOGY

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

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

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

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

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Complex nitrogen cycling in the spongeGeodia barretti

(2009) Friederike Hoffmann et al.   ENVIRONMENTAL MICROBIOLOGY

Evidence of nitrification and denitrification in high and low microbial abundance sponges

(2009) Marie-Lise Schläppy et al.   MARINE BIOLOGY

CERBERUS, a novel U-box protein containing WD-40 repeats, is required for formation of the infection thread and nodule development in the legume-Rhizobiumsymbiosis

(2009) Koji Yano et al.   PLANT JOURNAL

Functional diversity of ankyrin repeats in microbial proteins

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

Physiology, phylogeny andin situevidence for bacterial and archaeal nitrifiers in the marine spongeAplysina aerophoba

(2008) Kristina Bayer et al.   ENVIRONMENTAL MICROBIOLOGY

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

(2008) José R. de la Torre et al.   ENVIRONMENTAL MICROBIOLOGY

The functional roles of marine sponges

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

Ankyrin Repeat Proteins Comprise a Diverse Family of Bacterial Type IV Effectors

(2008) X. Pan et al.   SCIENCE