The role of tissue-specific microbiota in initial establishment success of Pacific oysters

Resistant Microbial Cooccurrence Patterns Inferred by Network Topology

(2015) Sari Peura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology

(2015) Ben Stenuit et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Bacteria-Mediated Effects of Antibiotics on Daphnia Nutrition

(2015) Elena Gorokhova et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis

(2015) Cléa Bauvais et al.   MARINE ENVIRONMENTAL RESEARCH

Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals

(2015) Guillaume Meisterhans et al.   MICROBIAL ECOLOGY

Adaptation to enemy shifts: rapid resistance evolution to local Vibrio spp. in invasive Pacific oysters

(2015) C. C. Wendling et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Interchange of entire communities: microbial community coalescence

(2015) Matthias C. Rillig et al.   TRENDS IN ECOLOGY & EVOLUTION

Cross-biome comparison of microbial association networks

(2015) Karoline Faust et al.   Frontiers in Microbiology

Crassostrea gigas mortality in France: the usual suspect, a herpes virus, may not be the killer in this polymicrobial opportunistic disease

(2015) Bruno Petton et al.   Frontiers in Microbiology

Commensal bacteria mediated defenses against pathogens

(2014) Michael C Abt et al.   CURRENT OPINION IN IMMUNOLOGY

International arrivals: widespread bioinvasions in European Seas

(2014) B.S. Galil et al.   ETHOLOGY ECOLOGY & EVOLUTION

The potential impact of climate change on the infectious diseases of commercially important shellfish populations in the Irish Sea--a review

(2014) A. F. Rowley et al.   ICES JOURNAL OF MARINE SCIENCE

Water fleas require microbiota for survival, growth and reproduction

(2014) Marilou P Sison-Mangus et al.   ISME Journal

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection

(2014) Ana Lokmer et al.   ISME Journal

Bivalve aquaculture transfers in Atlantic Europe. Part A: Transfer activities and legal framework

(2014) F. Muehlbauer et al.   OCEAN & COASTAL MANAGEMENT

Colonisation of the Non-Indigenous Pacific Oyster Crassostrea gigas Determined by Predation, Size and Initial Settlement Densities

(2014) Luke H. Hedge et al.   PLoS One

Short-Term Effect of Antibiotics on Human Gut Microbiota

(2014) Suchita Panda et al.   PLoS One

Persistence, Seasonal Dynamics and Pathogenic Potential of Vibrio Communities from Pacific Oyster Hemolymph

(2014) Carolin C. Wendling et al.   PLoS One

Fluvial network organization imprints on microbial co-occurrence networks

(2014) S. Widder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load: The Smile-Frown Transition

(2014) Rafael Pena-Miller et al.   PLOS BIOLOGY

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

(2014) Thomas S. B. Schmidt et al.   PLoS Computational Biology

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

(2014) Ryan J. Williams et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Host lifestyle affects human microbiota on daily timescales

(2014) Lawrence A David et al.   GENOME BIOLOGY

The Central Role of the Gut Microbiota in Chronic Inflammatory Diseases

(2014) Caroline Marcantonio Ferreira et al.   Journal of Immunology Research

DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure

(2014) Benjamin E. R. Rubin et al.   MicrobiologyOpen

Higher Water Temperature and Incubation under Aerobic and Microaerobic Conditions Increase the Recovery and Diversity of Arcobacter spp. from Shellfish

(2013) Arturo Levican et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Relative contribution of reproductive investment, thermal stress and Vibrio infection to summer mortality phenomena in Pacific oysters

(2013) Carolin C. Wendling et al.   AQUACULTURE

Disturbance induced decoupling between host genetics and composition of the associated microbiome

(2013) Karl Wegner et al.   BMC MICROBIOLOGY

Changes in the composition and diversity of the bacterial microbiota associated with oysters (Crassostrea corteziensis,Crassostrea gigasandCrassostrea sikamea) during commercial production

(2013) Natalia Trabal Fernández et al.   FEMS MICROBIOLOGY ECOLOGY

Exploring the hologenome concept in marine bivalvia: haemolymph microbiota as a pertinent source of probiotics for aquaculture

(2013) Florie Desriac et al.   FEMS MICROBIOLOGY LETTERS

Antimicrobial peptides in oyster hemolymph: The bacterial connection

(2013) Diane Defer et al.   FISH & SHELLFISH IMMUNOLOGY

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Control of pathogens and pathobionts by the gut microbiota

(2013) Nobuhiko Kamada et al.   NATURE IMMUNOLOGY

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

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

Till Death Do Us Part: Stable Sponge-Bacteria Associations under Thermal and Food Shortage Stresses

(2013) Lucía Pita et al.   PLoS One

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biotic Interactions, Rapid Evolution, and the Establishment of Introduced Species

(2012) Emily I. Jones et al.   AMERICAN NATURALIST

Lineage-dependent ecological coherence in bacteria

(2012) Alexander F. Koeppel et al.   FEMS MICROBIOLOGY ECOLOGY

Molecular analysis of the bacterial communities in the live Pacific oyster (Crassostrea gigas) and the influence of postharvest temperature on its structure

(2012) J. Fernandez-Piquer et al.   JOURNAL OF APPLIED MICROBIOLOGY

Density-dependent effects of an introduced oyster, Crassostrea gigas, on a native intertidal seagrass, Zostera marina 

(2012) E Wagner et al.   MARINE ECOLOGY PROGRESS SERIES

Molecular Analysis of Bacterial Microbiota Associated with Oysters (Crassostrea gigas and Crassostrea corteziensis) in Different Growth Phases at Two Cultivation Sites

(2012) Natalia Trabal et al.   MICROBIAL ECOLOGY

Phylogenetic Analysis Suggests That Habitat Filtering Is Structuring Marine Bacterial Communities Across the Globe

(2012) Mikael Pontarp et al.   MICROBIAL ECOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust 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

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

Bacterial Diversity Stabilizes Community Productivity

(2012) Nico Eisenhauer et al.   PLoS One

High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature

(2012) Martin J. Sergeant et al.   PLoS One

Impact of the Resident Microbiota on the Nutritional Phenotype of Drosophila melanogaster

(2012) Emma V. Ridley et al.   PLoS One

Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

(2012) Philip Francis Thomsen et al.   PLoS One

A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable

(2012) Jiri Hulcr et al.   PLoS One

Analysis of Stomach and Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana, USA

(2012) Gary M. King et al.   PLoS One

Anticipating Critical Transitions

(2012) M. Scheffer et al.   SCIENCE

mvabund- anRpackage for model-based analysis of multivariate abundance data

(2012) Yi Wang et al.   Methods in Ecology and Evolution

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Local Biotic Environment Shapes the Spatial Scale of Bacteriophage Adaptation to Bacteria

(2011) Britt Koskella et al.   AMERICAN NATURALIST

Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea

(2011) Dror Zurel et al.   ENVIRONMENTAL MICROBIOLOGY

Water quality assessment by means of HFNI valvometry and high-frequency data modeling

(2011) Mohamedou Sow et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

Invasion genetics of Pacific oyster Crassostrea gigas shaped by aquaculture stocking practices

(2011) Jenny Moehler et al.   JOURNAL OF SEA RESEARCH

Metabolic Robustness and Network Modularity: A Model Study

(2011) Petter Holme   PLoS One

Distance-based multivariate analyses confound location and dispersion effects

(2011) David I. Warton et al.   Methods in Ecology and Evolution

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

(2010) C. Manichanh et al.   GENOME RESEARCH

Population dynamics of Vibrio spp. associated with marine sponge microcosms

(2010) Maria Hoffmann et al.   ISME Journal

Association Between Environmental Microbiota and Indigenous Bacteria Found in Hemolymph, Extrapallial Fluid and Mucus of Anodonta cygnea (Linnaeus, 1758)

(2010) Filipa Antunes et al.   MICROBIAL ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon

(2010) M. C. Rea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

(2010) E. Thebault et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SYNTHESIS: Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence

(2009) Sam P. Brown et al.   Evolutionary Applications

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Robustness of the Bacterial Community in the Cabbage White Butterfly Larval Midgut

(2009) Courtney J. Robinson et al.   MICROBIAL ECOLOGY

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

The Origins of Ecological Diversity in Prokaryotes

(2008) Frederick M. Cohan et al.   CURRENT BIOLOGY

Re-emergence of Vibrio tubiashii in bivalve shellfish aquaculture: severity, environmental drivers, geographic extent and management

(2008) RA Elston et al.   DISEASES OF AQUATIC ORGANISMS

Host-specificity of environmentally transmitted Mycoplasma-like isopod symbionts

(2008) Sebastian Fraune et al.   ENVIRONMENTAL MICROBIOLOGY

Shift from native mussels to alien oysters: Differential effects of ecosystem engineers

(2008) Judith Kochmann et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

(2008) Nicole Dubilier et al.   NATURE REVIEWS MICROBIOLOGY

Diversity predicts stability and resource use efficiency in natural phytoplankton communities

(2008) Robert Ptacnik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A reverse search for antimicrobial peptides in Ciona intestinalis: Identification of a gene family expressed in hemocytes and evaluation of activity

(2007) Henning Fedders et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY