Cited by 670Aquaculture disease management and microbiotaAquaculture Nutrition and GrowthGut microbiota and health

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

Ghanbari, Mahdi, Kneifel, Wolfgang, Domig, Konrad J.·2015·Aquaculture

DOI 10.1016/j.aquaculture.2015.06.033

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Abstract

The fish gut microbiota contributes to digestion and can affect the nutrition, growth, reproduction, overall population dynamics and vulnerability of the host fish to disease; therefore, this microbial community is highly relevant for aquaculture practice. Recent advances in DNA sequencing technologies and bioinformatic analysis have allowed us to develop a broader understanding of the complex microbial communities associated with various habitats, including the fish gut microbiota. These recent advances have substantially improved our knowledge of bacterial community profiles in the fish intestinal microbiota in response to a variety of factors affecting the host, including variations in temperature, salinity, developmental stage, digestive physiology and feeding strategy. The goal of this review is to highlight the potential of next-generation sequencing platforms for analysing fish gut microbiota. Recent and promising results in this field are presented along with a focus on new perspectives and future research directions of fish gut microbial ecology.

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Li, J., Boonanuntanasarn, S., Kiatmontri, J., Kaewda, J., Manassila, P., Luo, Z., Pongsetkul, J., & Nakharuthai, C. (2025) · Aquaculture · doi:10.1016/j.aquaculture.2025.743235 · Cited by 3
Do Changes in Prey Community in the Environment Affect the Feeding Selectivity of Silver Carp (Hypophthalmichthys molitrix) in the Pearl River, China?
Xia, Y., Liu, Q., Zhu, S., Li, Y., Li, X., & Li, J. (2022) · Sustainability · doi:10.3390/su141811175 · Cited by 3
Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, Cyprinus carpio (Linn., 1758)
Bharti, M., Nagar, S., & Negi, R. K. (2023) · 3 Biotech · doi:10.1007/s13205-023-03747-0 · Cited by 3
“In spite of growing curiosity in vertebrate’s gut microbiome, understanding of microbial diversity composition and evolutionary dynamics of fishes is comparatively limited (Ghanbari et al. 2015; Tarnecki et al. 2019).”
Background
Gut microbiome variation based on 16S rRNA gene amplicon sequencing of the wild and domesticated broodstock populations of black tiger shrimp (Penaeus monodon) in the Indo-Pacific region
Wong, L. L., Deris, Z. M., Asaduzzaman, M., Wang, M., Liang, Y., Sung, Y. Y., & Iehata, S. (2023) · Ecological Genetics and Genomics · doi:10.1016/j.egg.2023.100204 · Cited by 3
Exposure to low levels of antidiabetic glibenclamide had no evident adverse effects on intestinal microbial composition and metabolic profiles in amphibian larvae
Liu, J., Meng, Q.-Y., Chen, Y., Yang, J., Gao, J.-F., & Lu, H. (2023) · Environmental Science and Pollution Research · doi:10.1007/s11356-023-30823-y · Cited by 3
“A loss of body mass has been documented to be linked with decreased Firmicutes abundance in some aquatic species (Ghanbari et al. 2015; Kang et al. 2022), but it did not seem apparent in our GLB-exposed tadpoles.”
Comparative analysis of gut microbiome in Pangasionodon hypopthalmus and Labeo catla during health and disease
Rathinam, R. B., Tripathi, G., Das, B. K., Jain, R. D., & Acharya, A. (2024) · International Microbiology · doi:10.1007/s10123-024-00494-x · Cited by 3
“Illumina Miseq sequencing was carried out with good coverage scores of the sequences, implied that the sequences recovered were adequate to analyze the diversity and other parameters (Ghanbari et al. 2015).”
Insights on Fish Gut Microbiome - A Review
Bhat, R. A., Dhillon, O., Hoque, F., & Sundaray, J. K. (2023) · JOURNAL OF AQUACULTURE · doi:10.61885/joa.v32.2023.294 · Cited by 4
“…key absorption of microbes in fish is from the surrounding water and diet and, as being such, this could be expected that the intestinal microbiota will vary between freshwater fish and seawater fish, representing different environmental compositions (Herlemann et al., 2011; Ghanbari et al., 2015).”
Background
Effect of Oregano Essential Oil on Growth and Composition of Gut Prokaryote Microbiota on Striped Bass (Morone saxatilis)
Trejo-Ramos, D. A., Rodríguez-Arana, C. O., Cruz‐Flores, R., & Hernández-Rodríguez, M. (2025) · Microorganisms · doi:10.3390/microorganisms13020264 · Cited by 6
Health Status of Marron, Cherax cainii (Austin, 2002) Fedcustomized Probiotic Bacillus mycoides
Ambas, I. (2017) · Journal of Aquaculture & Marine Biology · doi:10.15406/jamb.2017.06.00165 · Cited by 3
Bacterial composition in the toheroa (Paphies ventricosa), a threatened surf clam from Aotearoa (New Zealand)
Bennion, M., Ross, P., Lane, H. S., & McDonald, I. R. (2022) · Marine Biology · doi:10.1007/s00227-022-04025-y · Cited by 3
Investigation of the effects of rainbow trout (Oncorhynchus mykiss) skin mucus against indomethacin-induced gastric damage in rats
Bayir, H., Tacer‐Tanas, Ş., Yurdgülü, E. E., Albayrak, A., Toktay, E., & Bayır, Y. (2024) · Journal of Molecular Histology · doi:10.1007/s10735-024-10320-3 · Cited by 2
“MUC2 is a mucin protein that is one of the main components of mucus and a fundamental element of the intestinal chemical barrier (Ghanbari et al. 2015).”
The influence of sex on the intestinal flora of Procypris mera
Chen, L., Lin, H., Ren, J., Wu, W., Li, Z., Lin, Y., Li, Y., & Su, S. (2025) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2025.101464 · Cited by 2
Succession patterns, environmental connections, and assembly mechanisms of gut microbiota in the giant freshwater prawn (Macrobrachium rosenbergii) across lifespan
Zou, S., Zheng, Y., Yuan, J., Ni, M., Liu, M., Zhou, D., Gao, Q., Deng, M., Wang, R., & Zhang, X. (2025) · Aquaculture · doi:10.1016/j.aquaculture.2025.742927 · Cited by 2
Dietary supplementation of ethyl caffeate in hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂): study on growth-related gene expression and gut microbiota
Widodo, A. H. B., Huang, H., Dewi, N. R., Nugraha, M. A. R., & Nan, F. (2025) · Aquaculture International · doi:10.1007/s10499-025-02118-1 · Cited by 2
“Proteobacteria, along with Bacteroidetes and Firmicutes, constitute approximately 90% of the total gut microbiota across the various fish species that have been studied to date (Ghanbari et al. 2015); this finding is consistent with our results.”
A new insight on the application of phytosterols in the aquatic feed: Improve the growth and intestinal health of largemouth bass (Micropterus salmoides) fed the high starch diet
Ma, Y., Shi, H., Pan, Z., Liu, Y., Xia, M., Ouyang, P., Sun, F., Qu, K., Liu, Y., Deng, J., et al. (2025) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2025.101617 · Cited by 2
Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis
Feijão, E., Duarte, I. A., Pereira, M. H. N., Pascoal, P., Nunes, M., Tanner, S. E., Dias, R. P. M., Duarte, B., Matos, A. R., Figueiredo, A., et al. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.01508-25 · Cited by 2
“However, it has been reported that most of the gut bacteriome of fish is composed of bacteria with a high abundance of the phyla Pseudomonadota, Bacillota, and Bacteroidota (41), with carnivorous fish showing a higher abundance of Pseudo monadota and Bacillota than herbivorous species (13, 42).”
Modulation of Gut Microbiota, Intestinal Physiology, and Digestive Enzyme Levels by Duo‐Strain Probiotics in African Catfish ( Clarias gariepinus ) Challenged With Aeromonas hydrophila
Aini, N. L., Wahyuningsih, S. P. A., Achhlam, D. H., FATIMAH, F., Amin, M. H. F., & Do, H. D. K. (2025) · Aquaculture Nutrition · doi:10.1155/anu/6624613 · Cited by 2
“Biotic factors include genotype, physiological status, disease pathology, and lifestyle, while abiotic factors encompass environmental conditions [46].”
Immediate and Delayed Impacts of Alizarin Red S Dye on Salmo trutta Fry: Physiological and Fitness Responses
Račkauskas, S., Montvydienė, D., Jurgelėnė, Ž., Skrodenytė-Arbačiauskienė, V., Virbickas, T., Poviliūnas, J., & Rakauskas, V. (2025) · Fishes · doi:10.3390/fishes10120624 · Cited by 2
“By combining acute stress indicators, microbiome-related endpoints, growth and blood parameters with mark-retention checks, this study directly addresses priorities highlighted in recent syntheses on mass-marking optimization and fish microbiome research [21,28].”
Combined effects of glutamine dipeptide, plant essential oils, and Astragalus polysaccharide on growth performance, antioxidant capacity, immune function, and intestinal health in large yellow croaker (Larimichthys crocea)
Zhu, X., Zhan, Y., Chen, Y., Hang, Y., Wang, C., Mi, S., Zhang, J., Sun, M., Yuan, L., Lin, M., et al. (2025) · Aquaculture Reports · doi:10.1016/j.aqrep.2025.103283 · Cited by 2
Emamectin Benzoate-Induced Gut Dysbiosis in Asian Stinging Catfish: An Integrated Culture-Dependent and 16S rRNA Gene Sequencing Approach
Ghosh, S., Bag, S., SAHA, D., Sadhu, A., Roy, T., Nayak, S., Chatterjee, S., Mondal, K., Saha, N. C., Pastorino, P., et al. (2026) · Pollutants · doi:10.3390/pollutants6020030 · Cited by 2
“The gut microbiota contributes to the digestion of dietary components, synthesis of essential nutrients, modulation of immune responses, and protection against pathogenic microorganisms [3,4].”
Fish gut-water interface as a hotspot for the dissemination of antibiotic resistance genes across natural and aquaculture systems
Dolkar, P., Themchuirin, L., Sonia, N., Atri, A., Yadav, P., Siwach, S., Modeel, S., & Negi, R. K. (2026) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2026.100646 · Cited by 2
“These phyla have consistently been shown to constitute up to 90% of bacterial communities in aquatic and fish-associated environments (Ghanbari et al., 2015; Minich et al., 2020).”
Study of metagenomics of Barilius bendelisis (Hamilton, 1822) fish species
Sarkar, A. P., Das, S. R., & Basumatary, S. (2022) · Food Chemistry Advances · doi:10.1016/j.focha.2022.100031 · Cited by 2
Study of the characteristics of intestinal bacteria of little yellow croaker (Larimichthys polyactis) and big head croaker (Collichthys lucidus) from the Lyusi fishing ground
Chen, S., Xu, H., Zhang, S., & Yu, W. (2022) · Marine Biology Research · doi:10.1080/17451000.2022.2072893 · Cited by 2
“These methods are increasingly used in the study of fish, and research has found that this technique can be used to study low-abundance bacteria as well as the genetics and metabolism of species (Ghanbari et al. 2015).”
MethodResult
Analysis of intestinal flora and environmental microbial diversity of Takifugu rubripes
Ma, M., Ye, X., Zhang, S., Wang, X., & Qiu, X. (2022) · Israeli Journal of Aquaculture - Bamidgeh · doi:10.46989/001c.55683 · Cited by 2
“Firmicutes are related to carbohydrate metabolism and absorption and help the host to decompose related substances by producing various enzymes to promote the absorption of nutrients (Nuriel-Ohayon et al., 2016).”
BackgroundInfluential
CROSS SEASONAL INHERITANCE AND IMPACT OF AMBIENT WATER MICROBIOTA ON THE GUT MICROBIOTA OF RHINOGOBIO CYLINDRICUS GÜNTHER
CHEN, X. J., ZHU, Q. G., YANG, Z., ZHAO, N., & NI, J. J. (2022) · Applied Ecology and Environmental Research · doi:10.15666/aeer/2005_45394551 · Cited by 2
“The gut microbiota (GM) participates in various physiological processes, such as digestion (Ghanbari et al., 2015; Liu et al., 2016), growth (Li et al., 2019), metabolism (Butt and Volkoff, 2019), and immune response in fish (Galindo-Villegas et al., 2012; Stagaman et al., 2017).”
Background
Gut Microbes and Its Physiological Role in Fish: Adaptive Strategies for Climatic Variability
Kumari, K., & Nair, S. M. (2022) · Springer eBooks · doi:10.1007/978-981-19-5500-6_9 · Cited by 2
Metagenomic and isotopic signatures of the Amazon River plume into the southern red snapper fish (Lutjanus purpureus)
Nogueira, L. D. C., Asp, N. E., de Rezende, C. E., de Sousa, R. P. C., Barros, B., Paixão, R. V. S., Gatts, P. V., Thompson, C. C., Francini-Filho, R. B., Vallinoto, M., et al. (2023) · Estuarine Coastal and Shelf Science · doi:10.1016/j.ecss.2023.108440 · Cited by 2
Intestinal microbial profiling and immune responses of hybrid snakehead (Channa maculata ♀ × Channa argus ♂) challenged with Nocardia seriolae strain
Zhou, T., Cai, P., Li, J., Li, Z., & Dan, X. (2024) · Aquaculture Reports · doi:10.1016/j.aqrep.2024.102030 · Cited by 2
Roles of β-catenin in innate immune process and regulating intestinal flora in Qi river crucian carp (Carassius auratus)
Wu, L., Lv, X., Zhang, J., Wu, M., Zhao, X., Shi, X., Ma, W., Li, X., & Zou, Y. (2024) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2024.109521 · Cited by 2
Use of tunicate meal (pleated sea squirt Styela plicata) protein as a partial replacement of menhaden fish meal protein in the diet of juvenile Black Sea Bass
Delmaine, A. D., Watanabe, W. O., Carroll, P. M., & Alam, M. S. (2024) · North American Journal of Aquaculture · doi:10.1002/naaq.10334 · Cited by 2
Microbial Communities Associated with the Intestinal Tract of Grey Mullets from a Mediterranean Aquatic Environment
Floris, R., Sanna, G., Cecilia, T. S., Greta, B., De, P. F., Vezzi, A., & Nicola, F. (2024) · International Journal of Aquaculture and Fishery Sciences · doi:10.17352/2455-8400.000091 · Cited by 2
Environmental and population influences on mummichog ( Fundulus heteroclitus ) gut microbiomes
Ma, L., Hahn, M. E., Karchner, S. I., Nacci, D. E., Clark, B. W., & Apprill, A. M. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.00947-24 · Cited by 2
“Recent research has shown that external variables such as season, diet, and population density as well as host sex and immune system variation contribute to changes in fish gut microbiome richness and taxonomic composition (reviewed in reference [8]).”
Effects of the microbiome manipulation on survival and GI tract development of larval zebrafish (Danio rerio)
Padeniya, U. M., Septriani, S., Pataueg, A., & Brown, C. L. (2021) · E3S Web of Conferences · doi:10.1051/e3sconf/202132202016 · Cited by 2
Tail fell syndrome impacts intestinal microbiota in porcupinefish (Diodon hystrix)
Zhou, L., Jia, X., Liang, K., Zuo, X., Huang, F., Duan, X., Li, Z., Sang, S., & Wang, Q. (2023) · Frontiers in Marine Science · doi:10.3389/fmars.2023.1108737 · Cited by 2
“In view of this, 16S rRNA sequencing technology is widely used to study the composition of microbial communities in fish intestinal samples (Ghanbari et al., 2015; Wang et al., 2018).”
Background
Next-generation microbial drugs developed from microbiome's natural products
Bhattarai, K., Bhattarai, K., & Baral, B. (2021) · Advances in genetics · doi:10.1016/bs.adgen.2021.08.007 · Cited by 2
Assessing the functional diversity of herbivorous reef fishes using a compound-specific stable isotope approach
Tietbohl, M. D. (2016) · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · doi:10.25781/kaust-9s3hx · Cited by 2
Exploring the microbial diversity in oil-contaminated mangrove sediments using 16S rRNA metagenomicsPreprint
Ghanbari, M., Jami, M., Moghadam, M. S., & Domig, K. J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/735290 · Cited by 2
Characterization of the gut microbiota in the Anjak ( Schizocypris altidorsalis ), a native fish species of IranPreprint
Ghanbari, M., Jami, M., Shahraki, H., & Domig, K. J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/735241 · Cited by 2
“…sequencing (NGS) platforms offer the possibility to explore the diversity of microbial communities on an unprecedented scale, and indeed have been principally used to study the microbial ecology of a wide range of environments including the gut microbiota (Ghanbari et al. 2015; Kraler et al. 2016).”
BackgroundInfluential
Circadian dynamics of the teleost skin immune-microbiome interfacePreprint
Ellison, A., Wilcockson, D. C., & Cable, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.29.428758 · Cited by 2

Authors: Ghanbari, M., Kneifel, W., & Domig, K. J.
Affiliations: Zabol University (IR)
BOKU University (AT)
Corresponding author: Ghanbari, Mahdi
ORCID: Ghanbari, Mahdi
Kneifel, Wolfgang
Domig, Konrad J.
Venue: Aquaculture
Publisher: Elsevier BV
Published: 2015-11
Volume: 448
Pages: 464-475
ISSN: 0044-8486 (ISSN-L)
DOI: 10.1016/j.aquaculture.2015.06.033
OpenAlex: W1004644096
Cited by: 669
References: 90
Citations by year: 2026: 45 · 2025: 69 · 2024: 82 · 2023: 88 · 2022: 88 · 2021: 93 · 2020: 68 · 2019: 52 · 2018: 37 · 2017: 24 · 2016: 19 · 2015: 2
FWCI: 13.45
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Aquaculture (publishedVersion)
Topics: Life Sciences › Immunology and Microbiology › Immunology › Aquaculture disease management and microbiota
Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Aquaculture Nutrition and Growth
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords: fish gut microbiota, gut microbiota, microbial ecology, host factors, temperature, salinity, developmental stages, digestive physiology, feeding strategies

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

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