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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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“For example, studies have shown that diet influences the microorganisms associated with the gut of humans, fish, shrimps, and crabs (Nayak, 2010; Ursell et al., 2012; Sun and Xu, 2021).”
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The gut microbiota: a new perspective on the toxicity of malachite green (MG)
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“Many aspects of host physiology, including nutrition, stimulation of the immune system, protection against disease and gut-brain communication, are all profoundly influenced by the microbiota of the gastrointestinal tract (Foster et al., 2016; Nayak, 2010; Pérez et al., 2010).”
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“The genus Aeromonas, Pseudomonas, and Bacteroides were found to be dominant in majority freshwater fish intestine, followed by Enterobacteriaceae, Micrococcus, Acinetobacter, Clostridium, and others (Nayak, 2010).”
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“Data analysis revealed that the next most common phylum in the core gut microbiota after Tenericutes was Firmicutes, folowed by Proteobacteria (Figure 1B), as found in other studies on salmonids (Nayak, 2010; Gajardo et al., 2017).”
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“Functionally, gut microbiota exerts a profound influence on immunity, nutrient-processing capacity, disease susceptibility, growth, and reproduction of the host animals (Nayak, 2010; Ghanbari et al., 2015).”
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“Previous research reveals that Proteobacteria, Firmicutes, and Bacteroidetes are the dominant phyla of intestine of marine carnivorous fish (Nayak, 2010; Wang et al., 2018), which was consistent with our current results.”
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Biofilm consumption shapes the intestinal microbiota of shrimp (Penaeus vannamei )
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“Furthermore, the gut microbiota stimulates the proliferation and maturation of the intestinal epithelium, thereby increasing the absorptive surface area available for nutrient uptake (Nayak, 2010).”
Yu, Y., Lv, F., Wang, C., Wang, A., Zhao, W., & Yang, W. (2016) · Journal of the World Aquaculture Society · doi:10.1111/jwas.12308 · Cited by 21
Intestinal Microbiota in Large Yellow Croaker, Larimichthys crocea , at Different Ages
Wei, N., Wang, C., Xiao, S., Huang, W., Lin, M., Yan, Q., & Ma, Y. (2017) · Journal of the World Aquaculture Society · doi:10.1111/jwas.12463 · Cited by 21
Ghosh, K., & Ray, A. K. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-811412-4.00005-9 · Cited by 24
Deb, S., Das, L. M., & Das, S. K. (2020) · Archives of Microbiology · doi:10.1007/s00203-020-01997-7 · Cited by 21
“It is known that enzymes involved in carbohydrate metabolism are the most abundant in the digestive tract of omnivorous and herbivorous fish as compared to carnivorous fish (Ringø and Birkbeck 1999; Bairagi et al. 2002; Merrifield et al. 2010; Nayak 2010).”
BackgroundPulgar, R., Mandaković, D., Salgado, P., Venegas, L., Ortiz, D., Peña‐Neira, Á., & Wacyk, J. M. (2021) · Aquaculture · doi:10.1016/j.aquaculture.2021.737129 · Cited by 22
Goodrich, H. R., Wilson, R. W., Smullen, R. P., Barnes, A. C., & Franklin, C. E. (2021) · Aquaculture · doi:10.1016/j.aquaculture.2021.737400 · Cited by 23
Zaminhan‐Hassemer, M., Zagolin, G. B., Perazza, C. A., Barbosa, D. A., Menegídio, F. B., Coutinho, L. L., Tizioto, P. C., & Hilsdorf, A. W. S. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.738581 · Cited by 23
Tenets in Microbial Endocrinology: A New Vista in Teleost Reproduction
Haque, R., Das, I. I., Sawant, P. B., Chadha, N. K., Sahoo, L., Kumar, R., & Sundaray, J. K. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.871045 · Cited by 22
“According to (Nayak, 2010), the most frequently documented phyla in the salmonid gut microbiota are proteobacteria and firmicutes, suggesting that members of FIGURE 1 | Composition of microbiota in fish.”
BackgroundInfluentialZou, S., Ni, M., Liu, M., Xu, Q., Zhou, D., Gu, Z., & Yuan, J. (2023) · Folia Microbiologica · doi:10.1007/s12223-022-01027-7 · Cited by 21
“The intestinal tract of fish harbors abundant and highly diverse microbes, which constitute a complex and dynamic microbial ecosystem (Nayak 2010).”
BackgroundPang, A., Xin, Y., Xie, R., Wang, Z., Zhang, W. Y., & Tan, B. (2023) · Frontiers in Marine Science · doi:10.3389/fmars.2023.1170033 · Cited by 21
“…of the vast microbial communities in the intestines to maintain the integrity of the intestinal structure and function cannot be ignored, and harmful microbial infections resulting from an imbalance in the intestinal flora trigger the host to perform an inflammatory response (Nayak, 2010).”
BackgroundLobo, C., Tapia-Paniagua, S. T., Moreno-Ventas, X., Alarcón, F. J., Rodríguez, C., Balebona, M. C., Moríñigo, M. Á., & García-de-la-Banda, I. (2014) · Aquaculture · doi:10.1016/j.aquaculture.2014.06.011 · Cited by 21
Gaikwad, S., Shouche, Y. S., & Gade, W. (2017) · Indian Journal of Microbiology · doi:10.1007/s12088-017-0641-9 · Cited by 21
“are known to affect its physiology and thus their survival [8, 9], Ye et al.”
BackgroundLi, B., Chen, J., Wang, S., Qi, P., Chang, X., & Chang, Z. (2020) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2020.111124 · Cited by 21
The role of natural products on the immune status of freshwater fish
Awad, E. (2025) · Aquaculture International · doi:10.1007/s10499-025-02035-3 · Cited by 25
“Probiotics have been reported to interact with immune cells like phagocytic cells (monocytes, macrophages), neutrophils, and NK cells to induce innate immune responses (Nayak 2010; Seyed Hossein Hoseinifar et al. 2018).”
Martins, A. F. M., Pinheiro, T. L., Imperatori, A., Freire, S. M., Sá-Freire, L., Moreira, B. M., & Bonelli, R. R. (2018) · Aquaculture · doi:10.1016/j.aquaculture.2018.10.040 · Cited by 20
Turon, M., Uriz, M. J., & Martin, D. J. (2019) · mSystems · doi:10.1128/msystems.00148-19 · Cited by 20
Ma, S., Li, X., Sun, L., Fan, W., Chen, H., Yu, H., Zhou, W., Zhang, W., & Mai, K. (2021) · Aquaculture Nutrition · doi:10.1111/anu.13230 · Cited by 20
Clues from the intestinal mucus proteome of Atlantic salmon to counter inflammation
Kiron, V., Purushothaman, K., Fernandes, J. M. O., Sørensen, M., Vasanth, G. K., Lin, Q., Lin, Q., Lim, T. K., Dahle, D., Dias, J. P., et al. (2022) · Journal of Proteomics · doi:10.1016/j.jprot.2022.104487 · Cited by 20
Morshed, S. M., Chen, Y., Lin, C., Chen, Y., & Lee, T. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1097954 · Cited by 21
“Autochthonous microbes remain in close contact with the tissue and withstand bile acids, whereas allochthonous microbes remain in stool in a transient state (Nayak, 2010).”
BackgroundSingh, A., Vidaković, A., Hjertner, B., Krikigianni, E., Karnaouri, A., Christakopoulos, P., Rova, U., Dicksved, J., Baruah, K., & Lundh, T. (2023) · Aquaculture · doi:10.1016/j.aquaculture.2023.740002 · Cited by 20
“…physiology (Mussatto and Mancilha, 2007; Qiang et al., 2009; Sinha et al., 2011; Akrami et al., 2013); enhancement of growth and metabolic activity (Ortiz et al., 2013; Zhang et al., 2014); and orchestration of protective immune responses (Nayak, 2010; Guerreiro et al., 2016; Wang et al., 2018).”
BackgroundBacillus Sp. as Potential Probiotics for Use in Tilapia Fish Farming Aquaculture – A Review
Vijayaram, S., Chou, C., Razafindralambo, H. L., Ghafarifarsani, H., Divsalar, E., & Doan, H. V. (2024) · Annals of Animal Science · doi:10.2478/aoas-2024-0031 · Cited by 20
Godoy, F. A., Miranda, C. D., Wittwer, G., Aranda, C., & Calderón, R. (2015) · Annals of Microbiology · doi:10.1007/s13213-015-1076-3 · Cited by 20
“However, it has been found that these methods present several disadvantages and usually only detect aerobics and facultative anaerobic bacteria, but do not detect slow-growing bacteria (Spanggaard et al. 2000; Nayak 2010).”
InfluentialBacanu, G. M., & Oprea, L. (2013) · Cited by 20
Kashinskaya, E. N., Simonov, E., Izvekova, G. I., Николаевич, П. А., Andree, K. B., & Solovyev, M. M. (2019) · Journal of Fish Diseases · doi:10.1111/jfd.13096 · Cited by 20
He, Y., Guo, X., Tan, B., Dong, X., Yang, Q., Liu, H., Zhang, S., & Chi, S. (2020) · Aquaculture · doi:10.1016/j.aquaculture.2020.736154 · Cited by 20
Peixoto, M. J., Domingues, A., Batista, S., Gonçalves, G. S., Gomes, A., Cunha, S., Valente, L. M. P., Costas, B., & Ozório, R. O. A. (2018) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2018.09.045 · Cited by 20
Chen, H., Li, C., Liu, T., Chen, S., & Xiao, H. (2019) · Microbial Ecology · doi:10.1007/s00248-019-01409-4 · Cited by 20
The effect of spray‐dried porcine plasma on gilthead seabream (Sparus aurata) intestinal microbiota
Tapia-Paniagua, S. T., Balebona, M. C., Firmino, J. P., Rodríguez, C., Polo, J., Moríñigo, M. Á., & Gisbert, E. (2020) · Aquaculture Nutrition · doi:10.1111/anu.13039 · Cited by 20
Zhang, Y. X., Li, Z., Zhang, Y., Sun, K., Ren, N., & Li, M. (2022) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2022.114068 · Cited by 19
Fu, W.-J., Amenyogbe, E., Luo, J., Yang, E.-J., Huang, J., Chen, Y.-M., & Chen, G. (2022) · Aquaculture Reports · doi:10.1016/j.aqrep.2022.101348 · Cited by 19
Korry, B. J., & Belenky, P. A. (2023) · Animal Microbiome · doi:10.1186/s42523-023-00236-w · Cited by 18
“and trophic level The gut microbiota plays an important role in host digestion, increasing nutrient availability and uptake [5, 21, 76].”
BackgroundCadangin, J. F., Lee, J., Jeon, C.-Y., Lee, E., Moon, J., Park, S.-J., Hur, S., Jang, W.-J., & Choi, Y. (2024) · Aquaculture Reports · doi:10.1016/j.aqrep.2024.102027 · Cited by 19
Sun, Y., Yang, H., Ma, R., & Zhai, S. (2012) · Journal of the World Aquaculture Society · doi:10.1111/j.1749-7345.2012.00555.x · Cited by 19
Zhang, X., Peng, L., Wang, Y., Liang, Q., Deng, B., Li, W., Fu, L., Yu, D., Shen, W., & Wang, Z. (2014) · Aquaculture Nutrition · doi:10.1111/anu.12128 · Cited by 19
Effects of food-borne ZnO nanoparticles on intestinal microbiota of common carp (Cyprinus carpio L.)
Chupani, L., Bárta, J., & Zusková, E. (2019) · Environmental Science and Pollution Research · doi:10.1007/s11356-019-05616-x · Cited by 19
Attaya, A., Secombes, C. J., & Wang, T. (2020) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2020.06.051 · Cited by 19
Wang, B., Zhang, S., Dong, J., Li, Y., Jin, Y., Xiao, H., Wang, H., Fan, S., & Cui, M. (2021) · Environmental Pollution · doi:10.1016/j.envpol.2021.118539 · Cited by 19
Zhang, Z., Lv, Z., Zhang, W., Shao, Y., Zhao, X., Guo, M. Z., & Li, C. (2019) · Aquaculture · doi:10.1016/j.aquaculture.2019.734427 · Cited by 19
Kirschman, L. J., Khadjinova, A., Ireland, K., & Milligan‐McClellan, K. (2020) · Integrative and Comparative Biology · doi:10.1093/icb/icaa136 · Cited by 18
Bi, S., Lai, H., Guo, D., Liu, X., Wang, G., Chen, X., Liu, S., Yi, H., Su, Y., & Li, G. (2021) · Microorganisms · doi:10.3390/microorganisms9102125 · Cited by 18
“For example, the fish intestines are colonized by a diverse community of symbiotic and pathogenic microbes that are involved in various physiological processes, including the promotion of immune system development and the production of enzymes related with digestion [31,32].”
BackgroundResultLi, P., Hou, D., Zhao, H., Peng, K., Chen, B., Guo, H., & Cao, J. (2022) · Aquaculture Reports · doi:10.1016/j.aqrep.2022.101244 · Cited by 18
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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