Microbial Strategies for Survival in the Glass Sponge Vazella pourtalesii

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

(2020) J. Pamela Engelberts et al.   ISME Journal

Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach

(2020) Mario Moreno-Pino et al.   Scientific Reports

Mapping benthic ecological diversity and interactions with bottom-contact fishing on the Flemish Cap (northwest Atlantic)

(2020) F.J. Murillo et al.   ECOLOGICAL INDICATORS

Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida)

(2020) Georg Steinert et al.   Frontiers in Microbiology

Trophic Specialization Results in Genomic Reduction in Free-Living Marine Idiomarina Bacteria

(2019) Qi-Long Qin et al.   mBio

Glass sponge grounds on the Scotian Shelf and their associated biodiversity

(2019) N Hawkes et al.   MARINE ECOLOGY PROGRESS SERIES

Silicon isotopic systematics of deep-sea sponge grounds in the North Atlantic

(2019) Katharine R. Hendry et al.   QUATERNARY SCIENCE REVIEWS

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

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

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota

(2019) Shan Zhang et al.   mSystems

Oxygen and the Energetic Requirements of the First Multicellular Animals

(2018) Sally P Leys et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments

(2018) Daniel B Mills et al.   eLife

Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity

(2018) Leonardo T. Rosa et al.   Frontiers in Cellular and Infection Microbiology

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

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

(2018) L. Pita et al.   Microbiome

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich 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

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

(2018) Cindy J. Castelle et al.   NATURE REVIEWS MICROBIOLOGY

Predicted distribution of the glass sponge Vazella pourtalesi on the Scotian Shelf and its persistence in the face of climatic variability

(2018) Lindsay Beazley et al.   PLoS One

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

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

Inside Out: Archaeal Ectosymbionts Suggest a Second Model of Reduced-Genome Evolution

(2017) Trevor Nicks et al.   Frontiers in Microbiology

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

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

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

Dating early animal evolution using phylogenomic data

(2017) Martin Dohrmann et al.   Scientific Reports

Hydrography and Coastal Circulation along the Halifax Line and the Connections with the Gulf of St. Lawrence

(2016) M. Dever et al.   ATMOSPHERE-OCEAN

The distribution of deep-sea sponge aggregations in the North Atlantic and implications for their effective spatial management

(2016) Kerry-Louise Howell et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

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

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations

(2016) Amaia Sangrador-Vegas et al.   Database-The Journal of Biological Databases and Curation

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

(2016) Hannes Horn et al.   Frontiers in Microbiology

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

(2016) Volker Gloeckner et al.   BIOLOGICAL BULLETIN

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Drivers of epibenthic megafaunal composition in the sponge grounds of the Sackville Spur, northwest Atlantic

(2015) Lindsay Beazley et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

(2015) Barbara Bayer et al.   ISME Journal

Water masses and nutrient sources to the Gulf of Maine

(2015) David W. Townsend et al.   JOURNAL OF MARINE RESEARCH

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

Of early animals, anaerobic mitochondria, and a modern sponge

(2014) Marek Mentel et al.   BIOESSAYS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Natural Competence and the Evolution of DNA Uptake Specificity

(2014) J. C. Mell et al.   JOURNAL OF BACTERIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) Janine Kamke et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

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

Microbial Lifestyle and Genome Signatures

(2012)   CURRENT GENOMICS

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

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

Global Diversity of Sponges (Porifera)

(2012) Rob W. M. Van Soest et al.   PLoS One

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Hypoxia by degrees: Establishing definitions for a changing ocean

(2011) A.F. Hofmann et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Diversity and functional analysis of luxS genes in Vibrios from marine sponges Mycale laxissima and Ircinia strobilina

(2011) Jindong Zan et al.   ISME Journal

The archaeal cell envelope

(2011) Sonja-Verena Albers et al.   NATURE REVIEWS MICROBIOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Quorum-Sensing Network Architectures

(2009) Wai-Leung Ng et al.   Annual Review of Genetics

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

(2008) Kristina Bayer et al.   ENVIRONMENTAL MICROBIOLOGY

Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association

(2008) C. K. Chun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

(2008) Mircea Podar et al.   GENOME BIOLOGY