Cited by 1,073Aquaculture disease management and microbiotaAquaculture Nutrition and GrowthGut microbiota and health

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Role of gastrointestinal microbiota in fish

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Nayak, Sukanta K·2010·Aquaculture Research

DOI 10.1111/j.1365-2109.2010.02546.x

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Abstract

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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Oreochromis niloticus gastrointestinal microbiota affected by the infection with Staphylococcus haemolyticus and Providencia vermicola, two emerging pathogens in fish aquaculture
Medina‐Félix, D., Vargas‐Albores, F., Garibay-Valdéz, E., Martínez‐Córdova, L. R., & Martínez‐Porchas, M. (2023) · Aquaculture · doi:10.1016/j.aquaculture.2023.740529 · Cited by 4
Comparison of Growth, Gut Microbiota Composition, and Taste Sensory Profile of Abalone (Haliotis discus hannai) Fed Diets Formulated With Heat-Treated Or Fermented Seaweed (Sargassum horneri) Meal
Hur, S., Cadangin, J. F., Lee, S., Moon, J., Jang, W.-J., Nam, T., & Choi, Y. (2024) · Journal of Shellfish Research · doi:10.2983/035.043.0108 · Cited by 4
Chitosan-flocculated Picochlorum maculatum MACC3 as a functional feed for improved growth and health in guppies (Poecilia reticulata)
Kannukkarathi, T., Puthumana, J., Singh, I. S. B., & Joseph, V. (2025) · Algal Research · doi:10.1016/j.algal.2025.103968 · Cited by 4
Microbiological and physiological impacts of coconut oil microcapsule powder supplementation on Liza ramada
Basuini, M. F. E., Yahia, M. E., El-Hais, A. M., Soliman, A. A., Teiba, I. I., Badr, M. R., Zaki, M. A., Zaineldin, A. I., El-Ratel, I. T., Gewaily, M. S., et al. (2025) · Aquaculture · doi:10.1016/j.aquaculture.2025.742369 · Cited by 5
Effect of single-generation domestication of pikeperch on the performance of the offspring in conventional and pond recirculation aquaculture system
Péter, G., Lukić, J., Brlás-Molnár, Z., Ardó, L., Horváth, Z., Rónyai, A., Bársony, P., & Ljubobratović, U. (2023) · Aquaculture Reports · doi:10.1016/j.aqrep.2023.101702 · Cited by 4
Comparative effects of different dietary pectin types on growth performance and intestinal health in pearl gentian grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂)
Zhu, L., Meng, X., Wang, X., Fan, J., Tan, B., & Deng, J. (2024) · Aquaculture Reports · doi:10.1016/j.aqrep.2024.102547 · Cited by 4
Fish gut plasticity and its role as a potential mechanism for coping with warming and hypoxia
Goodrich, H. R. (2025) · Journal of Experimental Biology · doi:10.1242/jeb.249672 · Cited by 4
Efecto de medicamentos homeopáticos sobre crecimiento, supervivencia y microbiota gastrointestinal, en juveniles del pectínido Argopecten ventricosus.
Mazón‐Suástegui, J. M., Tovar‐Ramírez, D., Ortiz-Cornejo, N. L., Bernal, M. R. G., López‐Carvallo, J. A., Salas‐Leiva, J. S., & Abasolo‐Pacheco, F. (2019) · Revista Mvz Córdoba · doi:10.21897/rmvz.1536 · Cited by 4
“It is dominant in the GIT of herbivorous organisms and some Lactobacillus species can stimulate the immune system, protecting the host from invasion and establishment of pathogens (47).”
Background
Wood degradation by Panaque nigrolineatus, a neotropical catfish: diversity and activity of gastrointestinal tract lignocellulolytic and nitrogen fixing communities
Watts, J. E. M., McDonald, R. C., & Schreier, H. J. (2021) · Advances in botanical research · doi:10.1016/bs.abr.2021.05.005 · Cited by 4
Use of pre- and probiotics in finfish aquaculture
Iwashita, M. K. P., Addo, S., & Terhune, J. S. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-821598-2.00002-3 · Cited by 4
Interactions between Balantidium ctenopharyngodoni and microbiota reveal its low pathogenicity in the hindgut of grass carp
Zhao, W., Bu, X., Zhou, W., Zeng, Q., Qin, T., Wu, S., Li, W., Zou, H., Li, M., & Wang, G. (2024) · BMC Microbiology · doi:10.1186/s12866-023-03154-8 · Cited by 6
Inclusion of Sorghum in Cyprinus carpio L. Diet: Effects on Growth, Flesh Quality, Microbiota, and Oxidative Status
Barbacariu, C.-A., Dumitru, G., Rîmbu, C., Horhogea, C. E., Dîrvariu, L., Todirașcu-Ciornea, E., Șerban, D. A., & Burducea, M. (2024) · Animals · doi:10.3390/ani14111549 · Cited by 4
“The gut microbiome of fish is extremely complex, consisting of aerobic, facultative anaerobic, and obligate anaerobic microorganisms varying between 107 and 1011 cells/gram of gut contents, according to some authors [27,28].”
Background
Effects of Sacharomyces cereviceae Incorporated Diet on Growth Performance, Apparent Digestibility Coefficient of Protein and Survival Rate of Catfish (Pangasius hypothalamus)
Rachmawati, D., Samidjan, I., Nugroho, R. A., & Susilowati, T. (2019) · Aquacultura Indonesiana · doi:10.21534/ai.v20i1.136 · Cited by 4
“Meanwhile, Merrifield et al. (2010), Nayak (2010) and Welker and Lim (2011) suggested that imunostimulant improved digestibility and the absorption of nutrients, amino acid, vitamins and enzymes.”
Background
A preliminary study of the effect of total fishmeal replacement with different dietary sources on the gut microbiota of spotted rose snapper juvenile ( Lutjanus guttatus Steindachner, 1869)
Leyva‐López, N., Osuna‐García, E., Hernández, C., Gómez‐Gil, B., Soto-Rodríguez, S. A., & Guerrero, A. (2020) · Aquaculture Research · doi:10.1111/are.14823 · Cited by 6
Unique bacterial communities associated with components of an artificial aquarium ecosystem and their possible contributions to nutrient cycling in this microecosystem
Zhou, J. S., Cheng, J. F., Li, X. D., & Li, Y. H. (2022) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-022-03258-9 · Cited by 4
“2016); while Aeromonas bacteria were often detected in the healthy intestines of many fish species, and might contribute to the digestive function (Nayak 2010).”
Background
Effects of pre- and probiotics on pond production, growth and disease susceptibility of channel catfish Ictalurus punctatus and Nile tilapia Oreochromis niloticus
Addo, S. (2013) · Cited by 4
Tandem mass tag (TMT) proteomic analysis of rohu intestine against Edwardsiella tarda
Pinto, N., Nissa, M. U., Iqbal, G., Pratapa, M. G., Srivastava, S., & Goswami, M. (2025) · Aquaculture International · doi:10.1007/s10499-024-01805-9 · Cited by 3
“The early establishment of microbial load in fish intestines developed from the early larval stage and is continuously driven towards the achievement of a complex assemblage (Nayak 2010).”
Effects of Cold Stress on Skin Color, Immuno‐Antioxidant Function, Muscle Compositions, and Intestinal Microbiota of Red Tilapia During Overwintering
Yang, H.-R., Munyaradzia, H. B., Zhu, W.-B., Dong, Z., & Wang, L. (2025) · Aquaculture Research · doi:10.1155/are/9910096 · Cited by 3
Shifting seas and first feeds: gut microbiome dynamics in juvenile chum salmon (Oncorhynchus keta) and their climate vulnerability
Ghosh, S. K., Wong, M. K., Hyodo, S., & Hamasaki, K. (2025) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2025.100452 · Cited by 3
“…fish gut microbiota, and they are considered as an autochthonous community in the guts of both FW and SW environments (Roeselers et al., 2011; Wu et al., 2012; Kim et al., 2007; Nayak 2010; Wu et al., 2010), which is beneficial to digestion and immune functions (Ring ø , 2003; Ray et al., 2012).”
Depletion of Albendazole and Its Metabolites and Their Impact on the Gut Microbial Community Following Multiple Oral Dosing in Yellow River Carp (Cyprinus carpio haematopterus)
Liu, Y., Dai, Y., Zhang, Y., Wang, W.-R., Chen, Y., Jin, Y., Sun, L.-J., Li, S., Yang, F., Li, X., et al. (2025) · Fishes · doi:10.3390/fishes10080410 · Cited by 3
Functional Probiotic Intervention Reshapes Host Microbiota and Metabolite Profiles to Enhance Disease Resistance in Micropterus salmoides
Wang, H., Lin, L., Jin, W., Liang, Z., Hu, S., Zhu, A., & Jiang, L. (2025) · Marine Biotechnology · doi:10.1007/s10126-025-10514-0 · Cited by 3
Multi-omics interrogation of herbivorous phenotype acquisition in hybrid culter under a 30% crude protein diet
Wang, Y., Huang, J., Wen, M., Liang, H., Yang, Y., Qin, L., Shen, L., Huang, J., Huang, X., Mao, Z., et al. (2025) · BMC Genomics · doi:10.1186/s12864-025-12375-2 · Cited by 3
“Fish gut microbiota play a crucial role in immunoregulation, growth, and digestion [49].”
Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment—a review
Sundaray, J. K., Roy, D., Mohapatra, M., Mohanty, D., Das, I. I., & Parida, C. K. (2026) · Archives of Microbiology · doi:10.1007/s00203-025-04646-z · Cited by 3
“Probiotics can outcompete pathogens for adhesion sites and nutrients, produce antimicrobial compounds like bacteriocins and enzymes, and improve immune response of the host (Nayak 2010 ).”
Influential
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Combined effects of dietary licorice (Glycyrrhiza glabra) and ginger (Zingiber officinale) on growth performance, intestinal and hepatic health, antioxidant status, and gut microbiota composition in grey mullet (Liza ramada)
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Hong, J., Chen, M., Deng, Z., Li, Y., & Wang, Y. (2020) · Pakistan Journal of Zoology · doi:10.17582/journal.pjz/20190425190440 · Cited by 3
“Therefore, the stability of intestinal flora is of great significance for the healthy growth of the host (Ley et al., 2008; Nayak, 2010; Suez et al., 2014).”
Background
Unraveling the causation of flatulence on silver pomfret after starvation aquaculture involved in intestinal microbiota structure, enzyme, and histology
Nie, W., Xie, X., Wang, Y., & Zhu, S. (2024) · Aquaculture · doi:10.1016/j.aquaculture.2024.741822 · Cited by 3
Soybean Glycinin Reduced Growth Performance and Antioxidant Capacity and Caused Intestinal Inflammation and Microbiome Changes in Large Yellow Croaker (Larimichthys crocea)
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Comparative Analysis of Intestinal Microbiota in Wild, Domesticated, and Cultured Gymnocypris potanini firmispinatus
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“The equilibrium of intestinal microbiota is closely linked Biology 2024 , 13 , 983 2 of 15 to the health of the host [10].”
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Zhou, G., Wang, Y., Wang, H., Sun, T., Peng, R.-Q., Li, S., Peng, H., Wen, X., Zhu, X., Zhu, Y.-Q., et al. (2024) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2024.101408 · Cited by 3
Differences in the bacterial communities along the intestinal tract of juvenile channel (Ictalurus punctatus) and hybrid (I. punctatus× I. furcatus) catfish
Older, C. E., Goodman, P. M., Reifers, J. G., & Yamamoto, F. Y. (2025) · Physiological Genomics · doi:10.1152/physiolgenomics.00008.2025 · Cited by 3
Characteristics of Intestinal Microbiota and Host Gene Regulation in Coilia nasus Responding to Stress
Gao, J. L., Zhu, H., Gao, J., & Xu, G. (2025) · Antioxidants · doi:10.3390/antiox14060626 · Cited by 3
“The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/antiox14060626/s1, Figure S1: RNA-seq results verified via RT-qPCR; Table S1: primers used for RT-qPCR verification.”
Influential
Gut microbiota: a new frontier in understanding and protecting endangered plateau schizothorax fish
Pan, H., Liu, H., Liu, F., Xie, J., Zhou, Y., Zheng, Q., & Guo, M. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1592312 · Cited by 3
“In vertebrates, a large number of rich microorganisms in the intestine aggregate to form a complex ecosystem that participates in the growth and development process of the host (Nayak, 2010; Walter et al., 2011).”
GUT MICROBIOTA OF BIGHEAD CARP (ARISTICHTHYS NOBILIS) AND PADDLEFISH (POLYODON SPATHULA) AFFECTED BY THEIR DIETS
Wang, Q., Xiong, B., Guo-Qiang, L., YanQiu, S., & Hai-yan, L. (2016) · doi:10.7541/2016.105 · Cited by 3
Effect of Dietary Probiotics Isolated from the Gut of Tilapia, Oreochromis mossambicus (Peters, 1852) on its Growth Performance and Digestive Enzyme Activities
Mariyam, K. H., Greeshma, K. P., Ramesh, P. R., & Pushpalatha, E. (2021) · International Journal of Zoological Investigations · doi:10.33745/ijzi.2021.v07i01.005 · Cited by 3
“Enterobacter, Clostridium, and Saccharomyces species (Nayak, 2010).”
Quality, Safety and Regulatory Issues of Probiotics
Awad, E., von Wright, A., & Austin, B. P. (2022) · Springer eBooks · doi:10.1007/978-3-030-98621-6_14 · Cited by 3
Probiotics and Its Application in Aquaculture
Kumar, S., Radhakrishnan, D. K., Ali, I. A., & Nareshkumar, A. (2022) · Springer eBooks · doi:10.1007/978-981-19-0817-0_14 · Cited by 3
Motile Aeromonads as a Nile Tilapia Bacterial Infection: A Review on Prevalence, Molecular Characterization, Effect on Immune Response and Alternatives Control Measures
Ammar, A. M., Abdelgelel, S., Mohamed, B., & Gharib, A. A. E. A. (2023) · Zagazig Veterinary Journal/Zagazig Veterinary Journal (Online) · doi:10.21608/zvjz.2023.181478.1199 · Cited by 5
“immune response and higher growth performance than the untreated fish [99].”
Background
Immunohistochemical Evaluation of Histamine Levels and Hygienic Aspect of Little Tunny (Euthynnus alletteratus) Musculature at Different Environment Time and Temperature
Mohamed, W. A., Hassanen, E. I., Mansour, H. A., & Mahmoud, M. A. (2023) · Journal of Aquatic Food Product Technology · doi:10.1080/10498850.2023.2259900 · Cited by 3
“Natural intestinal microbiota plays a major role in fish health (Gómez and Balcázar 2008; Nayak 2010).”
Background
Finfish Microbiota and Direct-Fed Microbial Applications in Aquaculture
Bledsoe, J. W., & Small, B. C. (2023) · Springer eBooks · doi:10.1007/978-3-031-40512-9_10 · Cited by 4
Insights on Fish Gut Microbiome - A Review
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“Nayak (2010) featured the immunomodulatory movement of gut microflora in fish.”
Background
Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water
Herlemann, D. P. R., Tammert, H., Kivistik, C., Käiro, K., & Kisand, V. (2024) · MicrobiologyOpen · doi:10.1002/mbo3.1413 · Cited by 3
“…present bacteria are often responsible for influencing the host development, aiding digestion or supplementing the nutrient pool, supporting the immune system, and influencing both physiology and metabolism (Nayak, 2010; Nicolai et al., 2015; Pinheiro et al., 2015; Sommer & Bäckhed, 2013).”
Background
Impacts of weathered microplastic ingestion on gastrointestinal microbial communities and health endpoints in fathead minnows (Pimephales promelas)
Petersen, M., & Partridge, C. (2024) · Journal of Great Lakes Research · doi:10.1016/j.jglr.2024.102374 · Cited by 3
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“Furthermore, the gut microbiota influences fish metabolism and growth, provides resistance to stress by regulating the gut-brain axis, and reduces susceptibility to disease by competitively excluding pathogenic bacteria from colonization sites [9, 10].”
Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling
Singh, A. B., Paul, T., Shukla, S. P., Kumar, S., Kumar, S. H., Kumar, G., & Kumar, K. (2024) · Ecotoxicology · doi:10.1007/s10646-024-02817-0 · Cited by 3
“The gastrointestinal tract (GI) of a ﬁ sh consists of a dynamic microbial ecosystem providing a favorable ecological niche for microorganisms (Nayak 2010).”
Effect of Oregano Essential Oil on Growth and Composition of Gut Prokaryote Microbiota on Striped Bass (Morone saxatilis)
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“Furthermore, these bacteria are prevalent in the gut of marine fish not only due to their evolved relationships as potential symbiotic, mutualistic, or commensal microbiota but also because they have diverse, efficient virulence mechanisms to colonize the intestinal environment [76,77].”
Probiotic Supplements in Aquaculture: Latest Developments and Future Trends
Roy, N. C., Munni, M. J., Chowdhury, M. A., & Akther, K. R. (2021) · Springer eBooks · doi:10.1007/978-981-16-5195-3_16 · Cited by 3
Impact of copper and zinc mixture on bacterial flora of digestive tract of rainbow trout (oncorhynchus mykiss)
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Characterization of dominant and cellulolytic bacterial communities along the gut of silver carp Hypophthalmichthys molitrix during cyanobacterial blooms
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“The stability of this relationship is crucial for maintaining host health, including nutrition provision, developmental support, immune system promotion and infection prevention [22,41].”

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)
DOI: 10.1111/j.1365-2109.2010.02546.x
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
Licence: doi.wiley.com/10.1002/tdm_license_1.1 (tdm, 1903 d)
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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