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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Method
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Background
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Background
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Background
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BackgroundInfluential
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Puri, P., Singh, R., & Sharma, J. G. (2023) · Beneficial Microbes · doi:10.3920/bm2022.0087 · Cited by 10
Can black soldier fly meal in diets improve gut microbiota diversity, nutrient digestibility, and growth response of marine fish? A study on red sea bream Pagrus major
Oktay, O., Seong, T., Kabeya, N., Morioka, S. M., Liu, C.-M., Kobayashi, T., Shimoda, M., Satoh, S., & Haga, Y. (2024) · Fisheries Science · doi:10.1007/s12562-024-01807-9 · Cited by 9
“Biotic (e.g., genotype, physiological condition, pathobiology, lifestyle) and abiotic (e.g., environmental) factors) may influence the composition and diversity of gut microbiota, consequently influencing fish growth, nutrient utilization, and health (Ghanbari et al. 2015).”
The Effect of High Levels Carbohydrate on Intestinal Microbiota, Metabolites, and Health of Common Carp (Cyprinus carpio L.)
Xiong, J., Yang, L., Wang, L., Zhi, S., Zhao, M., Xu, C., Qu, L., Guo, X., Yan, X., Qin, C., et al. (2024) · Aquaculture Nutrition · doi:10.1155/2024/7631021 · Cited by 9
Advances in Aquaculture Genomics, Genetics, and Breeding: Enhancing Sustainability and Efficiency Through Cutting‐Edge Technologies
Dhillon, O., Rather, M. A., Ahmad, I., Bhat, I. A., & Ahmad, I. (2025) · Journal of Applied Ichthyology · doi:10.1155/jai/8884803 · Cited by 9
Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads
Colin, Y., Berthe, T., Molbert, N., Moreau-Guigon, E., Vivant, A.-L., Alliot, F., Collin, S., Goutte, A., & Petit, F. (2021) · Microbial Ecology · doi:10.1007/s00248-020-01650-2 · Cited by 10
Different Types of Non-Starch Polysaccharides Alter the Growth, Intestinal Flora and Serum Metabolite Profile of Grass Carp, Ctenopharyngodon idella
Liu, Y., Fu, X., Zhou, H., Fan, J., Huang, H., Deng, J., & Tan, B. (2022) · Metabolites · doi:10.3390/metabo12101003 · Cited by 9
“Notably, the core flora plays an essential role in maintaining the normal intestinal physiological function [68].”
Background
Black Soldier Fly Bioconversion to Cultivated Meat Media Components Using Blue Catfish Gut Microbiome
Timoneda, A., Amirvaresi, A., & Ovissipour, R. (2024) · Bioresource Technology Reports · doi:10.1016/j.biteb.2024.101834 · Cited by 9
Zeolite mediated processing of nitrogenous waste in the rearing environment influences gut and sediment microbial community in freshwater crayfish (Cherax cainii) culture
Foysal, M. J., Nguyen, T. T. T., Sialumano, M., Phiri, S., Chaklader, M. R., Fotedar, R. K., Gagnon, M. M., & Tay, C. Y. (2022) · Chemosphere · doi:10.1016/j.chemosphere.2022.134276 · Cited by 9
Effects of Pelleted and Extruded Feed on Growth Performance, Intestinal Histology and Microbiota of Juvenile Red Swamp Crayfish (Procambarus clarkii)
Wan, J., Xi, Q., Tang, J., Liu, T., Liu, C., Li, H., Gu, X., Shen, M., Zhang, M., Fang, J., et al. (2022) · Animals · doi:10.3390/ani12172252 · Cited by 9
“which indicates that these bacteria are closely associated with crucial functions of the intestine, including nutrient absorption, digestion, and immunity [46].”
Background
Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron
Bettarel, Y., Combe, M., Adingra, A., Ndiaye, A., Bouvier, T. C., Panfili, J., & Durand, J.-D. (2018) · Scientific Reports · doi:10.1038/s41598-018-29643-9 · Cited by 9
Parasitic Infection by Pseudocapillaria tomentosa is Associated with a Longitudinal Restructuring of the Zebrafish Gut MicrobiomePreprint
Gaulke, C. A., Martins, M. L., Watral, V. G., Kent, M. L., & Sharpton, T. J. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/076596 · Cited by 9
“The fish microbiome is shaped by several 300 factors including developmental stage, [37,38], chemical exposures [25], and diet [36].”
Background
Gut Microbiome Analysis In Adult Tropical Gars ( Atractosteus tropicus )Preprint
Méndez-Pérez, R., García-López, R., Bautista-López, J. S. B.-L., Vázquez-Castellanos, J. F., Peña‐Marín, E. S., Martínez‐García, R., Domínguez-Rodríguez, V. I., Adams, R. H., Baltierra-Trejo, E., Valdes, C. E. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/557629 · Cited by 9
“Considering the above-mentioned, fish core gut microbiota (CGMB) can influence nutrition, growth, reproduction, general population dynamics and the host’s vulnerability to diseases thus supporting a crucial role in aquaculture practice (Ghanbari et al. 2015).”
Background
Exploring the Efficacy of Pellitorine as an Antiparasitic Agent Against Argulus: Impacts on Antioxidant Levels and Immune Responses in Goldfish (Carassius auratus)
Boopathi, S., Kesavan, D., Sudhakaran, G., Priya, P. S., Haridevamuthu, B., Dhanaraj, M., Seetharaman, S., Almutairi, B. O., Arokiyaraj, S., Guru, A., et al. (2024) · Acta Parasitologica · doi:10.1007/s11686-024-00792-4 · Cited by 8
“The ornamental fish market is experiencing significant expansion among the various aquaculture sectors [2].”
White feces syndrome is closely related with hypoimmunity and dysbiosis in Litopenaeus vannamei
Kangze, X., Zhang, S., Pang, A., Wang, T., Dong, S., Zhikuan, X., Zhang, X., Liang, J., Fang, Y., Tan, B., et al. (2024) · Aquaculture Reports · doi:10.1016/j.aqrep.2024.102329 · Cited by 8
Microcystin exposure alters gut microbiota composition in fish: An in-Situ analysis of post-bloom effects in Hulun Lake, China
Shang, Y., Wu, X., Wang, X., Chen, Y., Dong, Y., Wei, Q., Pang, B., Wang, Q., Liu, G., Dou, H., et al. (2024) · Environmental Pollution · doi:10.1016/j.envpol.2024.125174 · Cited by 8
Effects of Chronic Thermal Stress on the Physiology, Metabolism, Histology, and Gut Microbiota of Juvenile Schizothorax grahami
Bai, S., Li, T., Kong, L., Bi, B., & Hu, Q. (2025) · Animals · doi:10.3390/ani15182749 · Cited by 8
“Fish gut microbiota is usually dominated by the phyla of Proteobacteria, Firmicutes, and Bacteroidetes, as well as the phyla of Fusobacteriota and Actinobacteria [42].”
Changes in the intestinal microbiota of farmed northern sheatfish (Silurus soldatovi) associated with natural bacterial infection
Zan, Z., Mao, Q., Han, Z., & Sun, J. (2023) · Journal of the World Aquaculture Society · doi:10.1111/jwas.13000 · Cited by 8
Bacterial networks in Atlantic salmon with Piscirickettsiosis
Coca, Y., Godoy, M., Pontigo, J. P., Caro, D., Maracaja‐Coutinho, V., Arias‐Carrasco, R., Rodríguez‐Córdova, L., de, M. M., Sáez-Navarrete, C. A., & Burbulis, I. E. (2023) · Scientific Reports · doi:10.1038/s41598-023-43345-x · Cited by 8
“Metagenomics data represents an inventory of the microorganisms present in a sample 17 .”
Background
Shark Microbiome Analysis Demonstrates Unique Microbial Communities in Two Distinct Mediterranean Sea Shark Species
Montemagno, F., Romano, C., Bastoni, D., Cordone, A., CASTRO, O. D., Stefanni, S. S., Sperone, E., & Giovannelli, D. (2024) · Microorganisms · doi:10.3390/microorganisms12030557 · Cited by 8
“…diversity of gut microbiomes, and the communities are 90% characterized by members of the phyla Proteobacteria, Bacteroidetes, and Firmicutes [10,11], varying in response to changing nutrition and across other body surfaces, like skin and gills, which is especially interesting in marine…”
Background
Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839)
Nurul, A. A. N., Danish‐Daniel, M., Okomoda, V. T., & Asma, N. A. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-10781-y · Cited by 8
Occurrence of Cyanobacteria and microcystins in hydroelectric reservoirs used for fish farming
Falcone-Dias, M. F., Rodrigues, M. V., Nielsen, J. L., de Jonge, N., Jørgensen, N. O. G., Alonso, D. P., David, G. S., da Silva, R. J., & Araújo, J. P. (2020) · Journal of Water and Health · doi:10.2166/wh.2020.089 · Cited by 8
Assessment of bacteriophage vB_Pd_PDCC-1 on bacterial dynamics during ontogenetic development of the longfin yellowtail (Seriola rivoliana)
Veyrand-Quirós, B., Guzmán-Villanueva, L. T., Reyes, A. G., Rodrı́guez-Jaramillo, C., Salas‐Leiva, J. S., Tovar‐Ramírez, D., Balcázar, J. L., & Quiróz-Guzmán, E. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-021-11223-z · Cited by 8
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“Besides, several other NGS techniques have been used to identify fish gut microbiome and/or content (as reviewed in Ghanbari et al., 2015).”
Method
Evaluating Methods of Preserving Aquatic Invertebrates for Microbiome Analysis
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The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota
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Interactive Effect of Dietary Heat-Killed Lactobacillus Plantarum L-137 and Berberine Supplementation on Intestinal Mucosa and Microbiota of Juvenile Black Sea Bream (Acanthopagrus Schlegelii)
Sagada, G., Wang, L., Xu, B., Sun, Y., & Shao, Q. (2023) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-023-10153-8 · Cited by 8
“According to Ghanbari et al. [53], up to 90% of intestinal microbiota phyla of different fish species consist of Firmicutes, Bacteroidetes, and Proteobacteria, which were included in the top 5 phyla of black sea beam from all the groups in this study, in addition to Spirochaetes and Cyanobacteria.”
Composition and potential functions of the dominant microbiota in deep-sea hagfish gut from the South China Sea
Lian, C., Zhu, F.-C., Wei, Z., & He, L. (2021) · Deep Sea Research Part I Oceanographic Research Papers · doi:10.1016/j.dsr.2021.103488 · Cited by 8
Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methodsPreprint
Anslan, S., Li, H., Künzel, S., & Vences, M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/651612 · Cited by 13
Efficacy of an Insect-Based Diet with Addition of Probiotics on Growth, Proximate Composition, Enzymatic Efficiency, and Immune Response of Nile Tilapia
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Mechanism of sturgeon intestinal inflammation induced by Yersinia ruckeri and the effect of florfenicol intervention
Yang, Y., Xu, S., He, H., Xia Shuang, Z. H. U., Liu, Y., Ai, X., & Chen, Y. (2024) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2024.116138 · Cited by 7
Black Soldier Fly Meal as a Gastrointestinal Tract Microbiota Remodelling Factor: A New Natural and Sustainable Source of Prebiotic Substances for Fish?
Rawski, M., Mazurkiewicz, J., Mikołajczak, Z., Kierończyk, B., Skrzypczak, P., Szymkowiak, P., & Józefiak, D. (2025) · Aquaculture Research · doi:10.1155/are/8852384 · Cited by 10
Gut microbiome composition and diversity of wild-caught and hatchery-bred milkfish (Chanos chanos) fry
Silvederio, G. X. L., Javellana, T. F., Genciana, A. B. N., Fontanilla, M. A. G., Traifalgar, R. F. M., Huervana, F. H., & del Castillo, C. S. (2025) · Journal of Genetic Engineering and Biotechnology · doi:10.1016/j.jgeb.2025.100520 · Cited by 7
Changes of the intestinal microbiota along the gut of Japanese Eel ( Anguilla japonica )
Zhu, P., Wong, M. K., Lin, X., Chan, T., Wong, C. K. C., Lai, K. P., & Tse, W. K. F. (2021) · Letters in Applied Microbiology · doi:10.1111/lam.13539 · Cited by 6
“In addition, some studies using the hindgut (or distal gut) as their sample descriptions were commonly found (Ringø et al. 2006; Desai et al. 2012; CardaDi eguez et al. 2014; Ghanbari et al. 2015; Givens et al. 2015).”
BackgroundMethod
Microbiome of fish
Arun, D., & Midhun, S. J. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-90261-8.00011-0 · Cited by 7
Effects of weaning American glass eels (Anguilla rostrata) with the formula diet on intestinal microbiota and inflammatory cytokines genes expression
Liang, Y., Liu, H., Zhai, S., Huang, L., Huang, W., Huang, B., Xu, J., Xiong, J., & Wang, B. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e16965 · Cited by 7
“Recent advances in modern biotechnology technique like 16S rDNA high throughput sequencing, along with the development of bioinformatics tools, have provided faster results and high-resolution insights into the characteristic of the microbial communities [18,22].”
Background
Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline
Sumithra, T. G., Sharma, S. R. K., Suresh, G., Suja, G., Prasad, V., Gop, A. P., Patil, P. K., & Gopalakrishnan, A. S. (2024) · Scientific Reports · doi:10.1038/s41598-024-75319-y · Cited by 8
Comparative analysis of Oreochromis niloticus responses to Chlorella vulgaris and Lactobacillus-fermented Azolla economic feed supplements in biofloc and green systems: An in silico evaluation of metabolic and physiological responses
Aboseif, A. M., Flefil, N. S., Taha, M. K. S., El-Dein, A. N., Ren, M., Liang, H., & Hussian, A.-E. M. (2024) · Aquaculture Reports · doi:10.1016/j.aqrep.2024.102596 · Cited by 7
Correlation between gut microbial diversity and flatulence of silver pomfret ( Pampus argenteus ) during ontogenesis
Zhang, M., Hu, J., Wang, Y., Le, Q., Xu, S., Ying, X., Ying, D., Yang, Y., Zhang, Y., Li, Y., et al. (2020) · Aquaculture Research · doi:10.1111/are.14650 · Cited by 7
Importance of Interkingdom Interactions Among Oral Microbiome Towards Caries Development – A Review
Balakrishnan, K., Sivanesan, D., Mohan, G., Gunthe, S. S., & Verma, R. S. (2021) · Journal of Immunological Sciences · doi:10.29245/2578-3009/2021/2.1211 · Cited by 6
Role of probiotics on the immunity of Nile tilapia Oreochromis niloticus: a review
Alves, A. P. D. C., Peconick, A. P., Cerozi, B. D. S., & Cyrino, J. E. P. (2022) · Aquaculture International · doi:10.1007/s10499-022-00881-z · Cited by 7
“Results of next-generation sequencing-method studies have shown that Proteobacteria, Bacteroidetes, Firmicutes, and Fusobacterium phyla comprise 90% of the intestinal microbiota of fish (Ghanbari et al. 2015; Egerton et al. 2018).”
Method
Gut microbiota of an Amazonian fish in a heterogeneous riverscape: integrating genotype, environment, and parasitic infections
Leroux, N., Sylvain, F., Holland, A., Val, A. L., & Derôme, N. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.02755-22 · Cited by 7
“From these, four usually stand out as the most important: environmental conditions, host diet, genotype, and physiological condition (i.e., developmental stage and state of health) (2, 5–7).”
Background

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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