Fish Gut Microbiome: Current Approaches and Future Perspectives

Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water

(2018) Zhimin Zhang et al.   Frontiers in Microbiology

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers

(2017) Abhijit Maji et al.   ENVIRONMENTAL MICROBIOLOGY

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish

(2017) Keaton Stagaman et al.   ISME Journal

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

(2017) A.M. Tarnecki et al.   JOURNAL OF APPLIED MICROBIOLOGY

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet

(2017) Hyunmin Koo et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Composition of Gut Microbiota in the Gibel Carp (Carassius auratus gibelio) Varies with Host Development

(2017) Xinghao Li et al.   MICROBIAL ECOLOGY

Bacterial Signatures of “Red-Operculum” Disease in the Gut of Crucian Carp (Carassius auratus)

(2017) Tongtong Li et al.   MICROBIAL ECOLOGY

High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion

(2017) Zhimin Zhang et al.   Frontiers in Microbiology

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes

(2017) Tongtong Li et al.   Frontiers in Microbiology

Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens

(2017) Shaun Nielsen et al.   PeerJ

Fermented Soybean Meal Increases Lactic Acid Bacteria in Gut Microbiota of Atlantic Salmon (Salmo salar)

(2017) Natalia Catalán et al.   Probiotics and Antimicrobial Proteins

Microbiome disruption and recovery in the fish Gambusia affinis following exposure to broad-spectrum antibiotic

(2017) Jeanette Carlson et al.   Infection and Drug Resistance

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures

(2017) Stéphanie Céline Michl et al.   PLoS One

Anti-Infective Effect of Adhesive Probiotic Lactobacillus in Fish is Correlated With Their Spatial Distribution in the Intestinal Tissue

(2017) Suxu He et al.   Scientific Reports

Effect of dietary probiotic supplementation on intestinal microbiota and physiological conditions of Nile tilapia (Oreochromis niloticus) under waterborne cadmium exposure

(2016) Qixiao Zhai et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

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

Alternative Protein Sources in the Diet Modulate Microbiota and Functionality in the Distal Intestine of Atlantic Salmon (Salmo salar)

(2016) Karina Gajardo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories

(2016) François-Joël Gatesoupe et al.   BMC MICROBIOLOGY

Injections of Predatory Bacteria Work Alongside Host Immune Cells to Treat Shigella Infection in Zebrafish Larvae

(2016) Alexandra R. Willis et al.   CURRENT BIOLOGY

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members

(2016) Shugeng Feng et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2016) Qingyun Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Multiplicity of Quorum Quenching Enzymes: A Potential Mechanism to Limit Quorum Sensing Bacterial Population

(2016) Shikha Koul et al.   INDIAN JOURNAL OF MICROBIOLOGY

Simple and Rapid Method for Detecting Biofilm Forming Bacteria

(2016) Vipin Chandra Kalia et al.   INDIAN JOURNAL OF MICROBIOLOGY

Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

(2016) Shikha Koul et al.   INDIAN JOURNAL OF MICROBIOLOGY

Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow troutOncorhynchus mykissfrom both farm and aquarium settings

(2016) P.P. Lyons et al.   JOURNAL OF APPLIED MICROBIOLOGY

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

(2016) Kamarul Zaman Zarkasi et al.   MICROBIAL ECOLOGY

Biofilm Formation and Detachment in Gram-Negative Pathogens Is Modulated by Select Bile Acids

(2016) Laura M. Sanchez et al.   PLoS One

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

(2016) Philipp Hennersdorf et al.   PLoS One

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes

(2016) Jacob W. Bledsoe 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

The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

(2016) Wei Song et al.   Biomed Research International

Isolation ofBdellovibriosp. from soil samples in Mexico and their potential applications in control of pathogens

(2016) Omotayo Opemipo Oyedara et al.   MicrobiologyOpen

Environment shapes the fecal microbiome of invasive carp species

(2016) Jessica J. Eichmiller et al.   Microbiome

Probiotic legacy effects on gut microbial assembly in tilapia larvae

(2016) Christos Giatsis et al.   Scientific Reports

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

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

(2015) E. Ringø et al.   AQUACULTURE NUTRITION

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

(2015) Karen E Sullam et al.   ISME Journal

The composition of the zebrafish intestinal microbial community varies across development

(2015) W Zac Stephens et al.   ISME Journal

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

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

(2015) Martin S Llewellyn et al.   ISME Journal

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

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes

(2015) Naseer Sangwan et al.   Environmental Microbiology Reports

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

(2015) Christos Giatsis et al.   Scientific Reports

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

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

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

Microbial biofilms and the human intestinal microbiome

(2015) Willem M de Vos   npj Biofilms and Microbiomes

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing

(2015) Marcia L. Hart 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

Diversity and activity of cellulolytic bacteria, isolated from the gut contents of grass carp (Ctenopharyngodon idellus) (Valenciennes) fed on Sudan grass (Sorghum sudanense) or artificial feedstuffs

(2014) Huan Li et al.   AQUACULTURE RESEARCH

The intestinal microbiome of fish under starvation

(2014) Jun Xia et al.   BMC GENOMICS

The biofilm mode of life boosts the anti-inflammatory properties ofLactobacillus

(2014) Aurélie Rieu et al.   CELLULAR MICROBIOLOGY

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

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

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

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

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

Intestinal bacterial community structure differs between healthy and inflamed intestines in Atlantic salmon (Salmo salar L.)

(2013) Felipe E. Reveco 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

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

(2013) Mengxin Xing et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

Microbes, Antimicrobials and Resistance: The Battle Goes On

(2013) V. C. Kalia   INDIAN JOURNAL OF MICROBIOLOGY

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

(2013) Lin Ye et al.   ISME Journal

Devosia lucknowensis sp. nov., a bacterium isolated from hexachlorocyclohexane (HCH) contaminated pond soil

(2013) Ankita Dua et al.   JOURNAL OF MICROBIOLOGY

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

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

(2013) Xuemei Li et al.   PLoS One

Higher Prevalence and Abundance of Bdellovibrio bacteriovorus in the Human Gut of Healthy Subjects

(2013) Valerio Iebba et al.   PLoS One

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

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

(2012) Atul R. Desai et al.   AQUACULTURE

Quorum sensing inhibitors: An overview

(2012) Vipin Chandra Kalia   BIOTECHNOLOGY ADVANCES

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring Located atop the Himalayan Ranges at Manikaran, India

(2012) V. Dwivedi et al.   JOURNAL OF BACTERIOLOGY

Host species as a strong determinant of the intestinal microbiota of fish larvae

(2012) Xuemei Li et al.   JOURNAL OF MICROBIOLOGY

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

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

Intestinal microbiota composition in fishes is influenced by host ecology and environment

(2012) SANDI WONG et al.   MOLECULAR ECOLOGY

The influence of diet on the gut microbiota

(2012) Karen P. Scott et al.   PHARMACOLOGICAL RESEARCH

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

(2012) Shangong Wu et al.   PLoS One

Comparative Metagenomic Analysis of Soil Microbial Communities across Three Hexachlorocyclohexane Contamination Levels

(2012) Naseer Sangwan et al.   PLoS One

Phylogenetic Analysis of Microbial Communities in Different Regions of the Gastrointestinal Tract in Panaque nigrolineatus, a Wood-Eating Fish

(2012) Ryan McDonald et al.   PLoS One

Quenching the quorum sensing system: potential antibacterial drug targets

(2011) Vipin Chandra Kalia et al.   CRITICAL REVIEWS IN MICROBIOLOGY

Evidence for a core gut microbiota in the zebrafish

(2011) Guus Roeselers et al.   ISME Journal

Bdellovibrios, potential biocontrol bacteria against pathogenic Aeromonas hydrophila

(2011) Haipeng Cao et al.   VETERINARY MICROBIOLOGY

Characterization of rainbow trout (Oncorhynchus mykiss) intestinal microbiota and inflammatory marker gene expression in a recirculating aquaculture system

(2010) Graeme S. Mansfield et al.   AQUACULTURE

Role of gastrointestinal microbiota in fish

(2010) Sukanta K Nayak   AQUACULTURE RESEARCH

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

Host–microbe interactions in the developing zebrafish

(2010) Michelle Kanther et al.   CURRENT OPINION IN IMMUNOLOGY

Probiotics and immunity: A fish perspective

(2010) S.K. Nayak   FISH & SHELLFISH IMMUNOLOGY

Human microbiomics

(2010) J. Rajendhran et al.   INDIAN JOURNAL OF MICROBIOLOGY

Isolation and characterization of new potential probiotic bacteria based on quorum-sensing system

(2010) W. Chu et al.   JOURNAL OF APPLIED MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Isolation of Bdellovibrio as Biological Therapeutic Agents Used For the Treatment of Aeromonas hydrophila Infection in Fish

(2009) W.-H. Chu et al.   Zoonoses and Public Health

A review on the interactions between gut microbiota and innate immunity of fish: Table 1

(2008) Geovanny D. Gómez et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Molecular Analysis of Microbiota Along the Digestive Tract of Juvenile Atlantic Salmon (Salmo salar L.)

(2008) P. Navarrete et al.   MICROBIAL ECOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH