Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii

Divergent paths in the evolutionary history of maternally transmitted clam symbionts

(2022) Maëva Perez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transcriptome landscapes that signify Botrylloides leachi (Ascidiacea) torpor states

(2022) Yosef Hyams et al.   DEVELOPMENTAL BIOLOGY

High live coral cover and incidence of a pink-spotted coral phenotype on remote reefs off Clipperton Island, Tropical Eastern Pacific

(2022) Claudia Pogoreutz et al.   MARINE BIOLOGY

Improved metagenome binning and assembly using deep variational autoencoders

(2021) Jakob Nybo Nissen et al.   NATURE BIOTECHNOLOGY

The bacterial composition associated with Atriolum robustum, a common ascidian from Xisha coral reef, China

(2021) Yong Liu et al.   SYMBIOSIS

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

(2021) Tjorven Hinzke et al.   eLife

Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

(2020) Kshitij Tandon et al.   ISME Journal

Antibiotic Resistance Profile, Outer Membrane Proteins, Virulence Factors and Genome Sequence Analysis Reveal Clinical Isolates of Enterobacter Are Potential Pathogens Compared to Environmental Isolates

(2020) Mitali Mishra et al.   Frontiers in Cellular and Infection Microbiology

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

(2020) Silas Kieser et al.   BMC BIOINFORMATICS

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Microbiome definition re-visited: old concepts and new challenges

(2020) Gabriele Berg et al.   Microbiome

The potential role of the gut microbiota in shaping host energetics and metabolic rate

(2020) Elle C. Lindsay et al.   JOURNAL OF ANIMAL ECOLOGY

GToTree: a user-friendly workflow for phylogenomics

(2019) Michael D Lee   BIOINFORMATICS

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

(2019) Dongwan D. Kang et al.   PeerJ

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia

(2018) James M. Wiebler et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

(2018) Simon Blanchoud et al.   Scientific Reports

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA

(2018) Vladimir Benes et al.   NATURE METHODS

Biological and Chemical Diversity of Ascidian-Associated Microorganisms

(2018) Lei Chen et al.   Marine Drugs

Symbiotic bacteria associated with ascidian vanadium accumulation identified by 16S rRNA amplicon sequencing

(2018) Tatsuya Ueki et al.   Marine Genomics

Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems

(2016) David G. Bourne et al.   Annual Review of Microbiology

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

(2016) Matthew J. Neave et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Understanding mechanism of sea cucumber Apostichopus japonicus aestivation: Insights from TMT-based proteomic study

(2016) Muyan Chen et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

(2016) Felix Sommer et al.   Cell Reports

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts

(2016) Lars Schreiber et al.   Frontiers in Microbiology

Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host

(2016) Jiun-Yan Ding et al.   Frontiers in Microbiology

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

(2016) Ian J. Miller et al.   Scientific Reports

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

Lipopolysaccharides from Commensal and Opportunistic Bacteria: Characterization and Response of the Immune System of the Host Sponge Suberites domuncula

(2015) Johan Gardères et al.   Marine Drugs

Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts

(2014) Kevin D. Kohl et al.   FEMS MICROBIOLOGY ECOLOGY

Ascidian photosymbiosis: Diversity of cyanobacterial transmission during embryogenesis

(2014) Euichi Hirose   GENESIS

The secret to a successful relationship: lasting chemistry between ascidians and their symbiotic bacteria

(2014) Eric W. Schmidt   INVERTEBRATE BIOLOGY

Natural volcanic CO2 seeps reveal future trajectories for host–microbial associations in corals and sponges

(2014) Kathleen M Morrow et al.   ISME Journal

Species specificity of symbiosis and secondary metabolism in ascidians

(2014) Ma Diarey B Tianero et al.   ISME Journal

The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota

(2014) Larry J. Dishaw et al.   PLoS One

Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snailAlviniconchawith chemosynthetic, γ-Proteobacterial symbionts

(2014) R. A. Beinart et al.   Environmental Microbiology Reports

Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine spongeArenosclera brasiliensis

(2014) Cintia P.J. Rua et al.   PeerJ

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

(2013) Y. Liao et al.   BIOINFORMATICS

IscR Is a Global Regulator Essential for Pathogenesis of Vibrio vulnificus and Induced by Host Cells

(2013) Jong Gyu Lim et al.   INFECTION AND IMMUNITY

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

(2013) Patrick M Erwin et al.   ISME Journal

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

(2013) David G Bourne et al.   ISME Journal

Diversity and antibacterial activity of bacteria cultured from MediterraneanAxinellaspp. sponges

(2013) M. Haber et al.   JOURNAL OF APPLIED MICROBIOLOGY

Bacterial Communities of the Gorgonian Octocoral Pseudopterogorgia elisabethae

(2013) Hebelin Correa et al.   MICROBIAL ECOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Correction: In-situ Effects of Eutrophication and Overfishing on Physiology and Bacterial Diversity of the Red Sea Coral Acropora hemprichii

(2013) Christian Jessen et al.   PLoS One

Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

(2013) Nathalie L. Forget et al.   MicrobiologyOpen

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

(2012) Hannah V. Carey et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability

(2012) Kathleen M. Morrow et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007

(2012) M. Nishijima et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY 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

Using species combinations in indicator value analyses

(2012) Miquel De Cáceres et al.   Methods in Ecology and Evolution

Microbial diversity of biofilm communities in microniches associated with the didemnid ascidian Lissoclinum patella

(2011) Lars Behrendt et al.   ISME Journal

Cyanobacterial Diversity and a New Acaryochloris-Like Symbiont from Bahamian Sea-Squirts

(2011) Susanna López-Legentil et al.   PLoS One

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis

(2011) M. S. Donia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rickettsial evolution in the light of comparative genomics

(2010) Vicky Merhej et al.   BIOLOGICAL REVIEWS

Intracellular Oceanospirillales bacteria inhabit gills of Acesta bivalves

(2010) Sigmund Jensen et al.   FEMS MICROBIOLOGY ECOLOGY

Response of Gut Microbiota to Fasting and Hibernation in Syrian Hamsters

(2009) K. Sonoyama et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

(2009) J.-B. Raina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

C. Elegans Are Protected from Lethal Hypoxia by an Embryonic Diapause

(2009) Dana L. Miller et al.   CURRENT BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ammonia-oxidizingCrenarchaeotaand nitrification inside the tissue of a colonial ascidian

(2008) Manuel Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Identification and characterization of a new conjugation/type IVA secretion system (trb/tra) of Legionella pneumophila Corby localized on two mobile genomic islands

(2007) Gernot Glöckner et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY