Exploring the interactions between the gut microbiome and the shifting surrounding aquatic environment in fisheries and aquaculture: A review

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker

(2022) Jun Zhu et al.   Microbiome

A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss)

(2022) Jacob Agerbo Rasmussen et al.   Microbiome

Culturing the uncultured microbial majority in activated sludge: A critical review

(2022) Yulin Zhang et al.   CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY

Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment

(2022) Genmei Lin et al.   WATER RESEARCH

The vital roles of blue foods in the global food system

(2022) Michelle Tigchelaar et al.   Global Food Security-Agriculture Policy Economics and Environment

Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species

(2022) Meghali Bharti et al.   ARCHIVES OF MICROBIOLOGY

Metagenomic signatures of transportation stress in the early life stages of cobia (Rachycentron canadum) to aid in mitigation strategies

(2022) T.G. Sumithra et al.   AQUACULTURE

Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient

(2022) Yongjing Guan et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Gut milieu shapes the bacterial communities of invasive silver carp

(2021) Himani Khurana et al.   GENOMICS

Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota

(2021) Fanshu Xiao et al.   npj Biofilms and Microbiomes

Response of bacterial community in sea cucumber Apostichopus japonicus intestine, surrounding water and sediment subjected to high-temperature stress

(2021) Luo Wang et al.   AQUACULTURE

Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

(2021) Ludek Sehnal et al.   Frontiers in Microbiology

Microbiota Diversity in Pearl Oyster Pinctada fucata martensii Intestine and Its Aquaculture Environment

(2021) Zhe Zheng et al.   Frontiers in Marine Science

Deep insight into bacterial community characterization and relationship in the pond water, sediment and the gut of shrimp (Penaeus japonicus)

(2021) Li Zhou et al.   AQUACULTURE

Immune and intestinal microbiota responses to aerial exposure stress in Chinese mitten crab (Eriocheir sinensis)

(2021) Kun Guo et al.   AQUACULTURE

Enrofloxacin induces intestinal disorders of metabolome and microbiome in American shad ( Alosa sapidissima )

(2021) Jia Du et al.   AQUACULTURE RESEARCH

Dynamic changes in microbial community structure in farming pond water and their effect on the intestinal microbial community profile in juvenile common carp (Cyprinus carpio L.)

(2021) Xiaojun Jing et al.   GENOMICS

Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview

(2021) Arvind D. Diwan et al.   JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION

The role of gut microbial community and metabolomic shifts in adaptive resistance of Atlantic killifish (Fundulus heteroclitus) to polycyclic aromatic hydrocarbons

(2021) Lauren K. Redfern et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Host habitat is the major determinant of the gut microbiome of fish

(2021) Pil Soo Kim et al.   Microbiome

Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank

(2021) Chang Liu et al.   Microbiome

Connection between the Gut Microbiota of Largemouth Bass (Micropterus salmoides) and Microbiota of the Pond Culture Environment

(2021) Qianfu Liu et al.   Microorganisms

The Impact of Intensive Fish Farming on Pond Sediment Microbiome and Antibiotic Resistance Gene Composition

(2021) Eglė Lastauskienė et al.   Frontiers in Veterinary Science

Therapeutic modulation of fish gut microbiota, a feasible strategy for aquaculture?

(2021) Francisco Vargas-Albores et al.   AQUACULTURE

Microplastics as an aquatic pollutant affect gut microbiota within aquatic animals

(2021) Weixin Li et al.   JOURNAL OF HAZARDOUS MATERIALS

Understanding host-microbiome-environment interactions: Insights from Daphnia as a model organism

(2021) Siddiq Akbar et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development

(2021) Pubo Chen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The response of sediment microbial communities to temporal and site-specific variations of pollution in interconnected aquaculture pond and ditch systems

(2021) Ming Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Response mechanism of gut microbiome and metabolism of European seabass (Dicentrarchus labrax) to temperature stress

(2021) Yanyun Liu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Characterization of tetracycline effects on microbial community, antibiotic resistance genes and antibiotic resistance of Aeromonas spp. in gut of goldfish Carassius auratus Linnaeus

(2020) Jia Jia et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Growth and health status of Pacific white shrimp, Litopenaeus vannamei, exposed to chronic water born cobalt

(2020) Chengzhuang Chen et al.   FISH & SHELLFISH IMMUNOLOGY

Relief of hypersaline stress in Nile tilapia Oreochromis niloticus by dietary supplementation of a host-derived Bacillus subtilis strain

(2020) Shangshang Tang et al.   AQUACULTURE

Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons

(2020) Xiaoxiao Shen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Growth and intestinal health of the red claw crayfish, Cherax quadricarinatus, reared under different salinities

(2020) Shubin Liu et al.   AQUACULTURE

Differential responses of gut microbiota of male and female fathead minnow (Pimephales promelas) to a short-term environmentally-relevant, aqueous exposure to benzo[a]pyrene

(2020) Abigail DeBofsky et al.   CHEMOSPHERE

Fish growth enhances microbial sulfur cycling in aquaculture pond sediments

(2020) Keke Zhang et al.   Microbial Biotechnology

Gut microbial metabolites as multi-kingdom intermediates

(2020) Kimberly A. Krautkramer et al.   NATURE REVIEWS MICROBIOLOGY

Healthy microbiome: a key to successful and sustainable shrimp aquaculture

(2020) Riya Rajeev et al.   Reviews in Aquaculture

Diazinon exposure produces histological damage, oxidative stress, immune disorders and gut microbiota dysbiosis in crucian carp (Carassius auratus gibelio)

(2020) Jiali Tang et al.   ENVIRONMENTAL POLLUTION

Comparative analysis of bacterial communities of water and intestines of silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) reared in aquaculture pond systems

(2020) Liu-Jiang Meng et al.   AQUACULTURE

Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish

(2019) Ruxia Qiao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Gut Microbiota and Energy Homeostasis in Fish

(2019) Robyn Lisa Butt et al.   Frontiers in Endocrinology

Insights into the intestinal microbiota of several aquatic organisms and association with the surrounding environment

(2019) Fulin Sun et al.   AQUACULTURE

Gut microbiota of aquatic organisms: A key endpoint for ecotoxicological studies

(2019) Lauris Evariste et al.   ENVIRONMENTAL POLLUTION

One Health - Cycling of diverse microbial communities as a connecting force for soil, plant, animal, human and ecosystem health

(2019) Ariena H.C. van Bruggen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microbiota comparison in the intestine of juvenile Chinese mitten crab Eriocheir sinensis fed different diets

(2019) Yunfei Sun et al.   AQUACULTURE

Morphological, microbiological and ultrastructural aspects of sepsis by Aeromonas hydrophila in Piaractus mesopotamicus

(2019) Fausto A. Marinho-Neto et al.   PLoS One

A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome

(2019) Thibault P.R.A. Legrand et al.   Reviews in Aquaculture

Microcystin-LR-induced changes of hepatopancreatic transcriptome, intestinal microbiota, and histopathology of freshwater crayfish (Procambarus clarkii)

(2019) Yu Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Isolation, Identification and Characteristics of Aeromonas veronii From Diseased Crucian Carp (Carassius auratus gibelio)

(2019) Feng Chen et al.   Frontiers in Microbiology

Gnotobiotic models: Powerful tools for deeply understanding intestinal microbiota-host interactions in aquaculture

(2019) Meiling Zhang et al.   AQUACULTURE

Accumulation of different shapes of microplastics initiates intestinal injury and gut microbiota dysbiosis in the gut of zebrafish

(2019) Ruxia Qiao et al.   CHEMOSPHERE

The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis

(2019) Ana Rita Almeida et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Impact of chronic exposure to trichlorfon on intestinal barrier, oxidative stress, inflammatory response and intestinal microbiome in common carp (Cyprinus carpio L.)

(2019) Xulu Chang et al.   ENVIRONMENTAL POLLUTION

Dietary lipid levels could improve growth and intestinal microbiota of juvenile swimming crab, Portunus trituberculatus

(2018) Peng Sun et al.   AQUACULTURE

Chronic exposure to low environmental concentrations and legal aquaculture doses of antibiotics cause systemic adverse effects in Nile tilapia and provoke differential human health risk

(2018) Samwel M. Limbu et al.   ENVIRONMENT INTERNATIONAL

Environmental concentrations of antibiotics impair zebrafish gut health

(2018) Li Zhou et al.   ENVIRONMENTAL POLLUTION

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout

(2018) D. Huyben et al.   JOURNAL OF APPLIED MICROBIOLOGY

Comparative analysis of the bacterial community compositions of the shrimp intestine, surrounding water and sediment

(2018) D. Hou et al.   JOURNAL OF APPLIED MICROBIOLOGY

The Gut Microbiota of Marine Fish

(2018) Sian Egerton et al.   Frontiers in Microbiology

Microbiota assemblages of water, sediment, and intestine and their associations with environmental factors and shrimp physiological health

(2018) Fei Huang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The gut microbiome and aquatic toxicology: An emerging concept for environmental health

(2018) Ondrej Adamovsky et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Fish Gut Microbiome: Current Approaches and Future Perspectives

(2018) Chandni Talwar et al.   INDIAN JOURNAL OF MICROBIOLOGY

Metagenomic insights into the structure and function of intestinal microbiota of the farmed Pacific white shrimp (Litopenaeus vannamei)

(2018) Shuo Gao et al.   AQUACULTURE

Biofilm consumption shapes the intestinal microbiota of shrimp (Penaeus vannamei )

(2018) Estefanía Garibay-Valdez et al.   AQUACULTURE NUTRITION

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment

(2018) Lanfen Fan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

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

Moving beyond microbiome-wide associations to causal microbe identification

(2017) Neeraj K. Surana et al.   NATURE

Biocontrol of Luminous Vibriosis in Shrimp Aquaculture: A Review of Current Approaches and Future Perspectives

(2017) Pragyan Dash et al.   Reviews in Fisheries Science & Aquaculture

Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions

(2017) Mark N. Read et al.   Frontiers in Immunology

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions

(2017) Fernanda Cornejo-Granados et al.   Scientific Reports

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

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

(2016) Qingyun Yan et al.   ENVIRONMENTAL MICROBIOLOGY

Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp

(2016) Jinyong Zhu et al.   MICROBIAL ECOLOGY

Characterizing bacterial communities in tilapia pond surface sediment and their responses to pond differences and temporal variations

(2016) Limin Fan et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Environment shapes the fecal microbiome of invasive carp species

(2016) Jessica J. Eichmiller et al.   Microbiome

Changes in intestinal bacterial communities are closely associated with shrimp disease severity

(2015) Jinbo Xiong et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A new view of the fish gut microbiome: Advances from next-generation sequencing

(2015) Mahdi Ghanbari et al.   AQUACULTURE

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

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

(2015) Christos Giatsis et al.   Scientific Reports

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

Arsenic Exposure Perturbs the Gut Microbiome and Its Metabolic Profile in Mice: An Integrated Metagenomics and Metabolomics Analysis

(2014) Kun Lu et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

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

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

(2014) Tongtong Li et al.   MICROBIAL ECOLOGY

Characterization of Intestinal Bacteria in Wild and Domesticated Adult Black Tiger Shrimp (Penaeus monodon)

(2014) Wanilada Rungrassamee et al.   PLoS One

Bacterial community of pond's water, sediment and in the guts of tilapia (Oreochromis niloticus) juveniles characterized by fluorescentin situhybridization technique

(2013) Alessandro Del'Duca et al.   AQUACULTURE RESEARCH

Next-generation sequencing technologies and their impact on microbial genomics

(2013) B. M. Forde et al.   Briefings in Functional Genomics

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

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

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

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Bacteriocin Production: a Probiotic Trait?

(2011) Alleson Dobson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Competitive interactions in Escherichia coli populations: the role of bacteriocins

(2010) Hadeel Majeed et al.   ISME Journal

Host–microbiota interactions within the fish intestinal ecosystem

(2010) T Pérez et al.   Mucosal Immunology

Epithelial cell proliferation in the developing zebrafish intestine is regulated by the Wnt pathway and microbial signaling via Myd88

(2010) S. E. Cheesman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The core gut microbiome, energy balance and obesity

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