Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach

Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

(2018) Mary T.H.D. Nguyen et al.   PeerJ

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

(2018) L. Pita et al.   Microbiome

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

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

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

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

Differential recycling of coral and algal dissolved organic matter via the sponge loop

(2016) Laura Rix et al.   FUNCTIONAL ECOLOGY

Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges

(2016) Zhiyong Li et al.   MARINE BIOTECHNOLOGY

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

(2016) Guofang Feng et al.   Scientific Reports

Emerging Sponge Models of Animal-Microbe Symbioses

(2016) Lucia Pita et al.   Frontiers in Microbiology

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas 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

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem

(2015) Susana Rodríguez-Marconi et al.   PLoS One

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality

(2014) Fan Zhang et al.   FEMS MICROBIOLOGY ECOLOGY

Host-specificity among abundant and rare taxa in the sponge microbiome

(2014) Julie Reveillaud et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Evidence of a Putative Deep Sea Specific Microbiome in Marine Sponges

(2014) Jonathan Kennedy et al.   PLoS One

Endemism and functional convergence across the North American soil mycobiome

(2014) J. M. Talbot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi indicated by metagenomics

(2014) Zhi-Yong Li et al.   Scientific Reports

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

(2013) Luis M. Rodriguez-R et al.   BIOINFORMATICS

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

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

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

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

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Functional convergence of microbes associated with temperate marine sponges

(2012) M. Ribes et al.   ENVIRONMENTAL MICROBIOLOGY

Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics

(2012) David Wilkins et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

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

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.

(2011) Leland Wilkinson   BIOMETRICS

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

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

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

(2011) Susanne Schmitt et al.   ISME Journal

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The functional roles of marine sponges

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

Dissolved carbon fixation by sponge–microbe consortia of deep water coral mounds in the northeastern Atlantic Ocean

(2008) FC van Duyl et al.   MARINE ECOLOGY PROGRESS SERIES