Microbiota associated with the skin, gills, and gut of the fish Parachondrostoma toxostoma from the Rhône basin

Host-microbiota interactions: from holobiont theory to analysis

(2019) Jean-Christophe Simon et al.   Microbiome

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes

(2018) Katherine R. Amato et al.   ISME Journal

Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs

(2018) Maelle Sevellec et al.   Microbiome

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity

(2018) Tamsyn M. Uren Webster et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors

(2018) Zoe A. Pratte et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake

(2018) E.N. Kashinskaya et al.   JOURNAL OF APPLIED MICROBIOLOGY

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild

(2018) Andrea M. Tarnecki et al.   MICROBIAL ECOLOGY

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

(2018) Marlène Chiarello et al.   Microbiome

Canals as ecological corridors and hybridization zones for two cyprinid species

(2018) Emmanuel Guivier et al.   HYDROBIOLOGIA

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species

(2017) Emmanuel Guivier et al.   MICROBIAL ECOLOGY

Progress in fish gastrointestinal microbiota research

(2017) An R. Wang et al.   Reviews in Aquaculture

The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire

(2017) Tyler J. Carrier et al.   Frontiers in Microbiology

Succession and Fermentation Products of Grass Carp (Ctenopharyngodon idellus) Hindgut Microbiota in Response to an Extreme Dietary Shift

(2017) Yao Tong Hao et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

The emergence of epitheliocystis in the upper Rhone region: evidence for Chlamydiae in wild and farmed salmonid populations

(2016) Maricruz Guevara Soto et al.   ARCHIVES OF MICROBIOLOGY

The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874)

(2016) Xuemei Li et al.   BMC MICROBIOLOGY

Environmental filtering decreases with fish development for the assembly of gut microbiota

(2016) Qingyun Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?

(2016) Antton Alberdi et al.   TRENDS IN ECOLOGY & EVOLUTION

The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels

(2016) Han Liu et al.   Scientific Reports

pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui (Colossoma macropomum)

(2016) François-Étienne Sylvain et al.   Scientific Reports

16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife

(2016) Maxime Galan et al.   mSystems

Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

(2015) Liam Lowrey et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

When Anthropogenic River Disturbance Decreases Hybridisation between Non-Native and Endemic Cyprinids and Drives an Ecomorphological Displacement towards Juvenile State in Both Species

(2015) Emmanuel Corse et al.   PLoS One

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Catchment-scale biogeography of riverine bacterioplankton

(2014) Daniel S Read et al.   ISME Journal

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra)

(2014) Katherine R. Amato et al.   MICROBIAL ECOLOGY

Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism?

(2014) Sébastien Boutin et al.   PLoS One

Pathogen bacteria adhesion to skin mucus of fishes

(2014) Said Benhamed et al.   VETERINARY MICROBIOLOGY

Individual diet has sex-dependent effects on vertebrate gut microbiota

(2014) Daniel I. Bolnick et al.   Nature Communications

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

Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus)

(2013) Mengxin Xing et al.   FEMS MICROBIOLOGY ECOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Genomic Porosity between Invasive Chondrostoma nasus and Endangered Endemic Parachondrostoma toxostoma (Cyprinidae): The Evolution of MHC IIB Genes

(2013) Andrea Šimková et al.   PLoS One

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites

(2012) Luke K. Ursell et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Global threats to human water security and river biodiversity

(2010) C. J. Vörösmarty et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE