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Role of gastrointestinal microbiota in fish
Open accessAbstract
The gastrointestinal (GI) tract of an animal consists of a very complex and dynamic microbial ecosystem that is very important from a nutritional, physiological and pathological point of view. A wide range of microbes derived from the surrounding aquatic environment, soil/sediment and feed are found to colonize in the GI tract of fish. Among the microbial groups, bacteria (aerobic, facultative anaerobic and obligate aneraobic forms) are the principal colonizers in the GI tract of fish, and in some fish, yeasts are also reported. The common bacterial colonizers in the GI tract of freshwater and marine fish include Vibrio, Aeromonas, Flavobacterium, Plesiomonas, Pseudomonas, Enterobacteriaceae, Micrococcus, Acinetobacter, Clostridium, Fusarium and Bacteroides, which may vary from species to species as well as environmental conditions. Besides, several unknown bacteria belonging to Mycoplasma, Arthrobacter, Brochothrix, Jeotgailbacillus, Ochrobactrum, Psychrobacter and Sejongia species in the GI tract of different fish species have now been identified successfully using culture-independent techniques. Gnotobiotic and conventional studies indicate the involvement of GI microbiota in fish nutrition, epithelial development, immunity as well as disease outbreak. This review also highlights the need for manipulating the gut microbiota with useful beneficial microbes through probiotic, prebiotic and synbiotic concepts for better fish health management.
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“When a fish consumes algal cells, the microbiome in the intestine digests the algal cell, releasing probiotic materials that inhibit pathogens (Austin, 2006;Ghanbari et al., 2015;Nayak, 2010).”
From Potential of microalgae as a sustainable feed ingredient for aquaculture (2021) · cites this paper as Nayak, 2010
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“Microalgae are known to have probiotic effects on fishes.”
From Potential of microalgae as a sustainable feed ingredient for aquaculture (2021) · cites this paper as Nayak, 2010
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BackgroundBi, S., Lai, H., Guo, D., Yi, H., Li, H., Liu, X., Chen, Q., Chen, J., Zhang, Z., Wei, X., et al. (2023) · BMC Ecology and Evolution · doi:10.1186/s12862-023-02120-2 · Cited by 2
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“Recent advances in gut - microbe interactions have highlighted the importance of gut microbiota in the growth and wellbeing of cultured fish (Nayak, 2010).”
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Baothman, O. A. S., A-Zahrani, S., & Al-Talhi, H. A. (2021) · Journal of Biological Research - Bollettino della Società Italiana di Biologia Sperimentale · doi:10.4081/jbr.2021.9519 · Cited by 2
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Behavioural types correlate with the gut microbiome in juvenile wild and reared gilthead seabream
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“As we know, the intestinal microbiota provides essential nutrients for the hosts [31,32], is involved in metabolism [33], and plays a vital role in immune regulation [34].”
Effect of noise on the behaviour and microbiome of a common temperate estuarine fish
Valenzisi, B., Gaston, T. F., Parsons, M. J., & Huggett, M. J. (2026) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2026.119347 · Cited by 1
Chen, W., Fan, Y., Huang, Y., He, J., & Liu, X. (2026) · Microorganisms · doi:10.3390/microorganisms14020504 · Cited by 1
“These microbes were mutualistic, processing complex plant glycans into simpler molecules, https://doi.org/10.3390/microorganisms14020504 and they aided in nutrient absorption, which was especially vital for herbivorous fish like gc [48].”
InfluentialVahdat, S., Asrami, M. B., & Fereidooni, A. E. (2026) · Aquaculture International · doi:10.1007/s10499-026-02470-w · Cited by 1
“…higher lysozyme activity in T7 aligns with findings by Wu et al. (2014), who reported enhanced lysozyme levels in biofloc systems supplemented with organic carbon, likely due to the proliferation of beneficial bacteria such as Bacillus , which are known to stimulate immune responses (Nayak 2010).”
Zhang, R., Mao, W., Liu, L., Wang, X., Li, H., & Zhu, H. (2026) · Aquaculture Nutrition · doi:10.1155/anu/2092050 · Cited by 1
Xu, L., Zhao, L., Liu, J., Min, S., Lin, X., Zhou, S., Liu, X., & Song, Z. (2026) · Aquaculture · doi:10.1016/j.aquaculture.2026.743892 · Cited by 1
Lanara, M., Asimakis, E. D., Mokhtar, N. B., Koutsodima, P., Batargias, C., Toskas, K., Stathopoulou, P. M., & Tsiamis, G. (2026) · Microorganisms · doi:10.3390/microorganisms14030708 · Cited by 1
Shen, X., Gibson‐Kueh, S., Nelson, S. P., Poon, Z. W. J., Terence, C., Vu, N. T., Carrai, M., Awate, S., Vij, S., Tan, M. R., et al. (2026) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2026.111344 · Cited by 1
García‐Márquez, J., Cerezo, I. M., Santos, R., Magalhães, R., Carvalho, A. P., Arijo, S., Oliva‐Teles, A., Serra, C. R. B. E. M., & Moríñigo, M. Á. (2026) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-026-13825-x · Cited by 1
“Although certain Aeromonas strains are associated with pathogenic infections (Fernández-Bravo and Figueras 2020), they are also commonly found in the intestines of freshwater fish, where they can play commensal roles (Nayak 2010).”
Fish microbiota and its role in fish physiology and diseases regulation
Muzzaffar, S., Mir, R. A., Mir, M. A., Noorani, I. A., & Khurshid, I. (2026) · Environmental Biology of Fishes · doi:10.1007/s10641-026-01843-7 · Cited by 2
“The fish gastrointestinal tract harbours obligate anaerobes, facultative anaerobes, and aerobes, with microbial densities ranging from 10 ⁷ to 10 11 cells per gram of intestinal content (Llewellyn et al. 2016; Nayak 2010).”
InfluentialGut microbial composition varies with host metabolic phenotype in juvenile Atlantic salmon
Lindsay, E. C., Barcan, A. S., Metcalfe, N. B., Bryce, A. L. E., McGinnity, P., Llewellyn, M. S., & Cheaib, B. A. (2026) · Journal of Experimental Biology · doi:10.1242/jeb.251523 · Cited by 1
“Diet influences gut microbiota composition (Green et al., 2013; Xia et al., 2014; Liu et al., 2022; Jin et al., 2022), and targeted use of probiotics or prebiotics may enhance energy recovery in aquaculture (Nayak, 2010; Llewellyn et al., 2014; Kazlauskaite et al., 2022; Abid et al., 2013).”
InfluentialXian, Y., Wang, F., Zou, Z., Wen, J., Chen, Y., Zhang, J., & Wang, Y. (2026) · Animals · doi:10.3390/ani16101542 · Cited by 1
Tran, H. Q., Stejskal, V., Regenda, J., & Elayaraja, S. (2026) · Italian Journal of Animal Science · doi:10.1080/1828051x.2026.2689210 · Cited by 1
Khmelevtsova, L. E., Prazdnova, E. V., Mazanko, M. S., Brislavskiy, Y., & Rudoy, D. V. (2026) · Microorganisms · doi:10.3390/microorganisms14081734 · Cited by 1
“Intestinal microbiota functions as a kind of “additional organ”, providing metabolic processes that are inaccessible to the fish organism itself [72].”
Probiotics in aquaculture: mechanisms of action and technological approaches (Part 1)
Manoyan, M., Ivanova, A. N., Панин, А. Н., & Ivanov, A. V. (2026) · Agrarian science · doi:10.32634/0869-8155-2026-409-08-53-65 · Cited by 1
Băcanu, M. G., Oprea, L., SANDU, G. C., Dinică, R. M., Maereanu, M., Măereanu, D., & Șerban, C. (2012) · DOAJ (DOAJ: Directory of Open Access Journals) · Cited by 1
Mojer, A. M. (2021) · Biological and Applied Environmental Research · doi:10.51304/baer.2021.5.1.98 · Cited by 1
“Nayak (2010) indicated that it is due to the abundance of bacteria, including Aeromonas spp., which are known to produce the protease enzyme in the gastrointestinal tract of fishes fed with S. cerevisiae.”
BackgroundFirmani, U. (2022) · Egyptian Journal of Aquatic Biology and Fisheries · doi:10.21608/ejabf.2022.241692 · Cited by 1
“Colonization and bacterial diversity in the digestive tract of fish usually depend on environmental conditions (Nayak, 2010).”
BackgroundThe role of farming practice in nutrient assimilation in small-scale tilapia farming
Parata, L., Noiney, J., Majzoub, M. E., Mazumder, D., Egan, S., & Sammut, J. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.739005 · Cited by 1
Indrawati, A., Safika, S., Ningrum, S., Aulia, K. T., Maheshwari, H., & Andriyono, S. (2022) · Al-mağallaẗ al-ʻirāqiyyaẗ li-l-ʻulūm al-bayṭariyyaẗ/Iraqi journal of veterinary sciences · doi:10.33899/ijvs.2022.135058.2440 · Cited by 1
“animal, while others are transient in the intestine (3).”
BackgroundNejad, A. J., & Yazdkhasti, M. (2023) · Jentashapir Journal of Cellular and Molecular Biology · doi:10.5812/jjcmb-136669 · Cited by 1
“The immunestimulating properties of probiotics can be significantly influenced by several factors, including their source, kind, quantity, and duration (25).”
BackgroundMahrouqi, H. A., Dobretsov, S., & Abdala-Daz, R. T. (2023) · Applied Environmental Biotechnology · doi:10.26789/aeb.2023.01.001 · Cited by 2
Introduction to Finfish Microbiome and Its Importance
Rajwade, J. M., Kulkarni, S. S., & Vanjari, J. (2023) · Springer eBooks · doi:10.1007/978-981-99-0852-3_1 · Cited by 1
Marine Fish Microbiome: Current Status and Future Perspectives
Pamanji, R., & Selvin, J. (2023) · Springer eBooks · doi:10.1007/978-981-99-5022-5_21 · Cited by 1
Sharma, P., Kapoor, N., & Langer, S. (2024) · Indian Journal of Microbiology · doi:10.1007/s12088-024-01286-7 · Cited by 2
“It has been verified by many researchers that the Proteobacteria aids in digestion in the healthy fishes [47].”
Sylvain, F., Thomas, A., & Derôme, N. (2024) · Springer eBooks · doi:10.1007/978-3-031-66822-7_12 · Cited by 1
Elabd, H., Wang, H., Othman, R. B., & Yao, H. (2025) · PLoS ONE · doi:10.1371/journal.pone.0315305 · Cited by 1
“The intestinal histology could be indicative to the effect of natural dietary supplementation on fish health status through assessing the immune response, growth performance, and biochemical profiles [9,12,13,15].”
Performance of jundiá larvae, Rhamdia quelen, fed on probiotic supplemented diets
Pinto, V. B., Ferreira, C. C., Oliveira, P. L. S., de Oliveira, R. R. B., Piedras, S. R. N., & Pouey, J. L. O. F. (2015) · Acta Scientiarum Animal Sciences · doi:10.4025/actascianimsci.v37i3.27106 · Cited by 1
“Moreover, by stimuli of the immune system, the response from the nonspecific immune system is faster if the organism is invaded by pathogens (Nayak, 2010; Picchietti et al., 2009).”
BackgroundChanges in microbiota of rainbow trout caused by sediments contamination
Šyvokienė, J. (2013) · Open Life Sciences · doi:10.2478/s11535-013-0236-3 · Cited by 1
“According to Nayak [9] the common bacterial colonizers in the gastrointestinal tract of freshwater and marine fish include Vibrio, Aeromonas, Flavobacterium, Plesiomonas, Pseudomonas, Enterobacteriaceae, Micrococcus, Acinetobacter, Clostridium, Fusarium and Bacteroides, which may vary from species to species as well a…”
BackgroundInfluentialNancy, B. A., Elumalai, K., Sivamani, P., Kandeepan, C., & Kalaimathi, R. V. (2014) · Cited by 1
Prasad, L., & Rangacharulu, P. V. (2015) · Journal of Applied and Natural Science · doi:10.31018/jans.v7i2.649 · Cited by 1
“(Nayak,2010).”
Nikolakakis, S., Dierckens, K. R., Bossier, P., & Adriaens, D. (2018) · Aquaculture Research · doi:10.1111/are.13716 · Cited by 1
Moon, C.-Y., Ko, J.-C., Kim, M., & Heo, M.-S. (2020) · Microbiology and Biotechnology Letters · doi:10.4014/mbl.1907.07013 · Cited by 1
Comparative Analysis of Intestinal Bacterial Communities in Healthy and Diseased Nibea albiflora
Zhu, X. P., Wei, N., Zhang, S. S., Lin, M., & Ma, Y. (2021) · Indian Journal of Animal Research · doi:10.18805/ijar.b-1393 · Cited by 1
Jlidi, M., Akremi, A., Brabra, W., Hmani, H., Daoud, L., BRAHIM, A. H., Suissi, N., & Ali, M. B. (2021) · MOL2NET International Conference on Multidisciplinary Sciences (MOL2NET) · doi:10.3390/mol2net-07-09217 · Cited by 1
Probiotic Bacteria in Gastro-Intestinal Tract of Hybrid Catfish Fed Insect Protein Meal
Mohammed, A.-P., Iloba, K. I., Adediran, A. A., Mohammed, Y. M., Chukwu, M. N., & Adamu, K. M. (2023) · Asian Journal of Fisheries and Aquatic Research · doi:10.9734/ajfar/2023/v21i2529 · Cited by 1
Peredo, A. M. (2012) · OakTrust (Texas A&M University Libraries) · Cited by 1
Brandsegg, H. (2015) · BIBSYS Brage (BIBSYS (Norway)) · Cited by 1
Song, S. J. (2013) · CU Scholar (University of Colorado Boulder) · Cited by 1
Yildirimer, C. (2017) · doi:10.15760/etd.3441 · Cited by 1
“It is now well documented that the vertebrate gastrointestinal (GI) tract harbors one of the most complex and dynamic microbial ecosystems (Nayak, 2010).”
BackgroundEffects of feeding yeasts on blood physiology and gut microbiota of rainbow trout
Huyben, D. C. (2017) · Epsilon Open Archive (Sveriges lantbruksuniversitet biblioteket (Swedish University of Agricultural Sciences)) · doi:10.13140/rg.2.2.18586.13761 · Cited by 1
Metadata
- Authors
- Nayak, S. K.
- Affiliations
- Nihon University (JP)
- Corresponding author
- Nayak, Sukanta K
- ORCID
- Nayak, Sukanta K
- Venue
- Aquaculture Research
- Publisher
- Hindawi Limited
- Published
- 2010-06-16
- Volume
- 41
- Issue
- 11
- Pages
- 1553-1573
- ISSN
- 1355-557X (ISSN-L)
- OpenAlex
- W1912394394
- Cited by
- 1,073
- References
- 240
- Citations by year
- 2026: 74 · 2025: 97 · 2024: 85 · 2023: 104 · 2022: 111 · 2021: 109 · 2020: 94 · 2019: 80 · 2018: 82 · 2017: 58 · 2016: 36 · 2015: 30 · 2014: 40 · 2013: 30 · 2012: 22
- FWCI
- 9.65
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Aquaculture Research (publishedVersion)
- Funders
- Nihon University
- Directorate for Biological Sciences
- 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
- gut microbiota, fish gut bacteria, fish nutrition, fish immunity, fish disease, probiotics, prebiotics, synbiotics, gut microbiota modulation, fish health management, culture-independent identification
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