Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

Influence of Fishmeal-Free Diets on Microbial Communities in Atlantic Salmon (Salmo salar) Recirculation Aquaculture Systems

(2016) Victor Schmidt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference

(2016) Meiling Zhang et al.   AQUACULTURE

Effects of fish meal replacement by soybean meal with supplementation of functional compound additives on intestinal morphology and microbiome of Japanese seabass (Lateolabrax japonicus)

(2016) Jie Wang et al.   AQUACULTURE RESEARCH

Effects of low-level dietary microalgae supplementation on the distal intestinal microbiome of farmed rainbow troutOncorhynchus mykiss(Walbaum)

(2016) Philip P Lyons et al.   AQUACULTURE RESEARCH

Microbial modulation of behavior and stress responses in zebrafish larvae

(2016) Daniel J. Davis et al.   BEHAVIOURAL BRAIN RESEARCH

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform

(2016) Fiona Fouhy et al.   BMC MICROBIOLOGY

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

(2016) Qingyun Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Thymol and Carvacrol Affect Hybrid Tilapia through the Combination of Direct Stimulation and an Intestinal Microbiota-Mediated Effect: Insights from a Germ-Free Zebrafish Model

(2016) Chao Ran et al.   JOURNAL OF NUTRITION

Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters

(2016) Philipp Hennersdorf et al.   MARINE POLLUTION BULLETIN

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet

(2016) Kamarul Zaman Zarkasi et al.   MICROBIAL ECOLOGY

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions

(2016) Philipp Hennersdorf et al.   PLoS One

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

Environment shapes the fecal microbiome of invasive carp species

(2016) Jessica J. Eichmiller et al.   Microbiome

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

(2016) Cian J. Hill et al.   Microbiome

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish

(2016) Christopher A. Gaulke et al.   PLoS One

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research

(2016) Karina Gajardo et al.   Scientific Reports

Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis

(2016) Tongtong Li et al.   Scientific Reports

Modulation of the intestinal microbiota and morphology of tilapia, Oreochromis niloticus, following the application of a multi-species probiotic

(2015) B . T. Standen et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story?

(2015) E. Ringø et al.   AQUACULTURE NUTRITION

Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow troutOncorhynchus mykiss(Walbaum) using next generation sequencing (NGS)

(2015) Philip P Lyons et al.   AQUACULTURE RESEARCH

Characterization of microbial communities in intensive GIFT tilapia (Oreochromis niloticus ) pond systems during the peak period of breeding

(2015) Limin Fan et al.   AQUACULTURE RESEARCH

Study of the microbiome of the intestine of the Comephorus dybowski korotneff, 1904

(2015) N. L. Bel’kova et al.   BIOLOGY BULLETIN

Selection in the host structures the microbiota associated with developing cod larvae (Gadus morhua)

(2015) Ingrid Bakke et al.   ENVIRONMENTAL MICROBIOLOGY

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

(2015) Chris CR Smith et al.   ISME Journal

The composition of the zebrafish intestinal microbial community varies across development

(2015) W Zac Stephens et al.   ISME Journal

The biogeography of the atlantic salmon (Salmo salar) gut microbiome

(2015) Martin S Llewellyn et al.   ISME Journal

A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods

(2015) E.N. Kashinskaya et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparison of the gut microbiomes of 12 bony fish and 3 shark species

(2015) CE Givens et al.   MARINE ECOLOGY PROGRESS SERIES

Community assembly of a euryhaline fish microbiome during salinity acclimation

(2015) Victor T. Schmidt et al.   MOLECULAR ECOLOGY

Diet strongly influences the gut microbiota of surgeonfishes

(2015) Sou Miyake et al.   MOLECULAR ECOLOGY

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene

(2015) G. Estruch et al.   PLoS One

Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes

(2015) Laura Baldo et al.   PLoS One

Bacterial community structure in the intestinal ecosystem of rainbow trout (Oncorhynchus mykiss) as revealed by pyrosequencing-based analysis of 16S rRNA genes

(2015) Miray Etyemez et al.   RESEARCH IN VETERINARY SCIENCE

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut

(2015) Sandi Wong et al.   mBio

The impact of rearing environment on the development of gut microbiota in tilapia larvae

(2015) Christos Giatsis et al.   Scientific Reports

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Comparison of the gut microbiomes of 12 bony fish and 3 shark species

(2015) CE Givens et al.   MARINE ECOLOGY PROGRESS SERIES

Impact of a novel protein meal on the gastrointestinal microbiota and the host transcriptome of larval zebrafish Danio rerio

(2015) Eugene Rurangwa et al.   Frontiers in Physiology

Selective Manipulation of the Gut Microbiota Improves Immune Status in Vertebrates

(2015) Ana Montalban-Arques et al.   Frontiers in Immunology

Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure

(2015) Adrienne B Narrowe et al.   Microbiome

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

(2015) Alan W. Walker et al.   Microbiome

Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach

(2015) Marty Kwok-Shing Wong et al.   BMC GENOMICS

A Comparison of the Beneficial Effects of Live and Heat-Inactivated Baker’s Yeast on Nile Tilapia: Suggestions on the Role and Function of the Secretory Metabolites Released from the Yeast

(2015) Chao Ran et al.   PLoS One

The development of the gut microbiota in rainbow trout (Oncorhynchus mykiss) is affected by first feeding and diet type

(2014) H.-C. Ingerslev et al.   AQUACULTURE

The intestinal microbiome of fish under starvation

(2014) Jun Xia et al.   BMC GENOMICS

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

(2014) Daniel I. Bolnick et al.   ECOLOGY LETTERS

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

Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss)

(2014) Hans-Christian Ingerslev et al.   FISH & SHELLFISH IMMUNOLOGY

Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salarL.) within a commercial mariculture system

(2014) K.Z. Zarkasi et al.   JOURNAL OF APPLIED MICROBIOLOGY

Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond?

(2014) X.M. Li et al.   JOURNAL OF APPLIED MICROBIOLOGY

Characterization of the gut microbiota of three commercially valuable warmwater fish species

(2014) A.M. Larsen et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparative Analysis of the Intestinal Bacterial Communities in Different Species of Carp by Pyrosequencing

(2014) Tongtong Li et al.   MICROBIAL ECOLOGY

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

(2014) Daniel I. Bolnick et al.   MOLECULAR ECOLOGY

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

The Impact of Different DNA Extraction Kits and Laboratories upon the Assessment of Human Gut Microbiota Composition by 16S rRNA Gene Sequencing

(2014) Nicholas A. Kennedy et al.   PLoS One

The Gut Microbial Community of Midas Cichlid Fish in Repeatedly Evolved Limnetic-Benthic Species Pairs

(2014) Paolo Franchini et al.   PLoS One

The Colonization Dynamics of the Gut Microbiota in Tilapia Larvae

(2014) Christos Giatsis et al.   PLoS One

Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries

(2014) Martin S. Llewellyn et al.   Frontiers in Microbiology

Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata)

(2014) Konstantinos A. Kormas et al.   MicrobiologyOpen

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Aquacultured Rainbow Trout (Oncorhynchus mykiss) Possess a Large Core Intestinal Microbiota That Is Resistant to Variation in Diet and Rearing Density

(2013) S. Wong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluation of the presence and efficiency of potential probiotic bacteria in the gut of tilapia (Oreochromis niloticus) using the fluorescent in situ hybridization technique

(2013) Alessandro Del'Duca et al.   AQUACULTURE

Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location

(2013) Bastiaan Star et al.   BMC MICROBIOLOGY

Fish gut microecosystem: a model for detecting spatial pattern of microorganisms

(2013) Jiajia Ni et al.   CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY

Pyrosequencing survey of intestinal microbiota diversity in cultured sea bass (Dicentrarchus labrax) fed functional diets

(2013) Miguel Carda-Diéguez et al.   FEMS MICROBIOLOGY ECOLOGY

Prebiotic effects of arabinoxylan oligosaccharides on juvenile Siberian sturgeon (Acipenser baerii) with emphasis on the modulation of the gut microbiota using 454 pyrosequencing

(2013) Zahra Geraylou et al.   FEMS MICROBIOLOGY ECOLOGY

Effects of dietary arabinoxylan-oligosaccharides (AXOS) and endogenous probiotics on the growth performance, non-specific immunity and gut microbiota of juvenile Siberian sturgeon (Acipenser baerii)

(2013) Zahra Geraylou et al.   FISH & SHELLFISH IMMUNOLOGY

Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish

(2013) Lin Ye et al.   ISME Journal

Microbial population dynamics in the faeces of wood-eating loricariid catfishes

(2013) N. Di Maiuta et al.   LETTERS IN APPLIED MICROBIOLOGY

Gut Microbiota Contributes to the Growth of Fast-Growing Transgenic Common Carp (Cyprinus carpio L.)

(2013) Xuemei Li et al.   PLoS One

Dietary soybean protein concentrate-induced intestinal disorder in marine farmed Atlantic salmon, Salmo salar is associated with alterations in gut microbiota

(2013) Timothy J. Green et al.   VETERINARY MICROBIOLOGY

Intestinal microbiota of gibel carp (Carassius auratus gibelio) and its origin as revealed by 454 pyrosequencing

(2013) Shan-Gong Wu et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss)

(2012) Atul R. Desai et al.   AQUACULTURE

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

(2012) KAREN E. SULLAM et al.   MOLECULAR ECOLOGY

Composition, Diversity, and Origin of the Bacterial Community in Grass Carp Intestine

(2012) Shangong Wu 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

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

The Gut Microbiota

(2012) K. Mueller et al.   SCIENCE

Inter-individual variation in the dominant intestinal microbiota of reared Atlantic cod (Gadus morhuaL.) larvae

(2011) Anders Jón Fjellheim et al.   AQUACULTURE RESEARCH

Beyond the Venn diagram: the hunt for a core microbiome

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Evidence for a core gut microbiota in the zebrafish

(2011) Guus Roeselers et al.   ISME Journal

Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.)

(2011) Maartje AHJ van Kessel et al.   AMB Express

Microbial diversity of intestinal contents and mucus in yellow catfish (Pelteobagrus fulvidraco)

(2010) Shangong Wu et al.   AQUACULTURE

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

Microbial manipulations to improve fish health and production – A Mediterranean perspective

(2010) Arkadios Dimitroglou et al.   FISH & SHELLFISH IMMUNOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Identification of adherent microbiota in the stomach and intestine of emperor red snapper (Lutjanus sebaeCuvier) using 16S rDNA-DGGE

(2009) Zhigang Zhou et al.   AQUACULTURE RESEARCH

Towards the human intestinal microbiota phylogenetic core

(2009) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

The core gut microbiome, energy balance and obesity

(2009) Peter J. Turnbaugh et al.   JOURNAL OF PHYSIOLOGY-LONDON

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation

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

Determination of fish origin by using 16S rDNA fingerprinting of bacterial communities by PCR-DGGE: An application on Pangasius fish from Viet Nam

(2007) Doan Duy Le Nguyen et al.   FOOD CONTROL