Petrozavodsk, Россия
Petrozavodsk, Россия
Petrozavodsk, Россия
Petrozavodsk, Россия
Intestinal microbiome of commercial aquatic species is an important fish farming factor that prevents or reduces economic losses. Heterotrophic bacteria that inhabit intestinal mucosa are involved in digestion, vitamin synthesis, immune modulation, and resistance to pathogens. Age-related changes in the composition of heterotrophic bacterial flora affect health status, nutrient absorption efficiency, and growth rate during ontogenesis. Most studies focus on the luminal microbiota, while the mucosal layer remains understudied despite its reliable impact on the immune system. The current lack of data on the agerelated bacterial dynamics limits the development of age-specific diet strategies and disease prevention. This article presents data on the correlation between the age of rainbow trout (Parasalmo mykiss (Walbaum, 1792)) and the composition of cultured heterotrophic microflora. The research featured 40 fish aged from one to two years and grown on fish farms in the Republic of Karelia, Russia. The bacteria isolated from their intestinal mucosa were identified using standard microbiological methods. The analysis involved the morphotype and biochemical activity, as well as the tinctorial and cultural characteristics of the isolates. The species identification relied on the MALDI-TOF technology. The indices of dominance (Simpson, Berger–Parker), evenness (Pielou), diversity (Shannon), and richness (Margalef, Menhinick) made it possible to reveal that the heterotrophic component of the rainbow trout intestinal bacteria was a stable microbial community with a predominance of Bacillaceae and Enterobacteriacae enterobacteria, as well as Gram-negative non-fermentative bacteria. The index values corresponded to moderate α-diversity, which is typical of natural communities that tend to combine several abundant species with some rare taxa. These results may help develop a scientific system for managing the gastrointestinal microflora of commercial fish to improve their health and productivity.
Aquaculture, bacterial flora, biodiversity, heterotrophs, intestinal microflora, rainbow trout, Salmonidae, cage culture
1. D’Agaro E, Gibertoni P, Esposito S. Recent trends and economic aspects in the rainbow trout (Oncorhynchus mykiss) Sector. Applied Science. 2022;12(17):8773. https://doi.org/10.3390/app12178773
2. Wilfart A, Garcia-.Launay F, Terrier F, Soudé E, Aguirre P, et al. A step towards sustainable aquaculture: Multiobjective feed formulation reduces environmental impacts at feed and farm levels for rainbow trout. Aquaculture. 2023;562:738826. https://doi.org/10.1016/j.aquaculture.2022.738826
3. Duman M, Altun S, Saticioglu IB, Romalde JL. A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022. Journal of Fish Diseases. 2025;48(9):e13886. https://doi.org/10.1111/jfd.13886
4. Banerjee G, Ray AK. Bacterial symbiosis in the fish gut and its role in health and metabolism. Symbiosis. 2017;72:1–11. https://doi.org/10.1007/s13199-016-0441-8
5. Sugita H, Ito Y. Identification of intestinal bacteria from Japanese flounder (Paralichthys olivaceus) and their ability to digest chitin. Letters in Applied Microbiology. 2006;43(3):336–342. https://doi.org/10.1111/j.1472-765x.2006.01943.x
6. Spor A, Koren O, Lee R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nature Reviews Microbiology. 2011;9:279–290. https://doi.org/10.1038/nrmicro2540
7. Nayak SK. Role of gastrointestinal microbiota in fish. Aquaculture Research. 2010;41(11):1553–1573. https://doi.org/10.1111/j.1365-2109.2010.02546.x
8. Ringø E, Zhou Z, Vecino JLG, Wadsworth S, Romero J, et al. Effects of dietary components on the gut microbiota of aquatic animals: A never-ending story? Aquaculture Nutrition. 2016;22(2):219–282. https://doi.org/10.1111/anu.12346
9. Morozova MA, Lartseva LV. Microbial communities of the hydro-ecosystem of the Lower Don and Taganrog Bay. Natural Sciences. 2012;(2):50–56. (In Russ.)
10. Zaitseva KV, Dokolin DA, Zlobin IV. Intestinal microbiocenos of rainbow trout in the conditions of a cage farm. Agrarian Bulletin of the Urals. 2022;(12):42–53. (In Russ.) https://doi.org/10.32417/1997-4868-2022-227-12-42-53
11. Zueva MS, Miroshnikova EP, Arinzhanov AE, Kilyakova YuV. The effect of probiotics on the elemental composition of muscle tissue in carp. Animal Husbandry and Fodder Production. 2023;106(2):8–20. (In Russ.) https://doi.org/10.33284/2658-3135-106-2-8
12. Izvekova GI, Izvekov EI, Plotnikov AO. Symbiotic microflora of fish in different ecological groups. Bulletin of the Russian Academy of Sciences. Biology Series. 2007;(6):728–737.
13. Sidorova NA, Karpenko LYu, Bakhta AA, Savushkin AI, Nikonov IN. Comparative analysis of intestinal intestinal microflora of rainbow trout selected from various fish farms of the republic Karelia. International Journal of Veterinary Medicine. 2024;(1):172–183. (In Russ.) https://doi.org/10.52419/issn2072-2419.2024.1.172
14. Germanova MA, Sidorova NA. Diversity of fish indigenous microflora and its role in the development of non-specific resistance. Current Issues of Veterinary Medicine in Laboratory Diagnostics: Proceedings of the International Scientific and Practical Conference dedicated to the 100th Anniversary of Professor V.V. Rudakov. St. Petersburg, 2023:66–67. (In Russ.)
15. Hovda MB, Lunestad BT, Fontanillas R, Rosnes JT. Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquaculture. 2007;272(1–4):581–588. https://doi.org/10.1016/j.aquaculture.2007.08.045
16. Kuzmina VV. Digestive processes in fish. New facts and hypotheses. Yaroslavl: Filigree; 2018, 300 p. (In Russ.) https://elibrary.ru/AXSWLH
17. Li S, Sang C, Turchini GM, Wang A, Zhang J, et al. Starch in aquafeeds: The benefits of a high amylose to amylopectin ratio and resistant starch content in diets for the carnivorous fish, largemouth bass (Micropterus salmoides). British Journal of Nutrition. 2020;124(11):1145–1155. https://doi.org/10.1017/S0007114520002214
18. Denev S, Staykov Y, Moutafchieva R, Beev G. Microbial ecology of the gastrointestinal tract of fish and the potential application of prebiotics and probiotics in finfish aquaculture. International Aquatic Research. 2009;(1):1–29.
19. Robertson PAW, O'Dowd C, Burrells C, Williams P, Austin B. Use of Carnobacterium sp. as a probiotic for Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss, Walbaum). Aquaculture. 2000;185(3–4):235–243. https://doi.org/10.1016/S0044-8486(99)00349-X
20. Minich JJ, Petrus S, Michael JD, Michael TP, Knight R, et al. Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. mSphere. 2020;5(3):e00401-20. https://doi.org/10.1128/mSphere.00401-20
21. Borges N, Keller-Costa T, Sanches-Fernandes GMM, Louvado A, Gomes NCM, et al. Bacteriome structure, function, and probiotics in fish larviculture: The good, the bad, and the gaps. Annual Review of Animal Biosciences. 2021;9:423–452. https://doi.org/10.1146/annurev-animal-062920-113114
22. Li X, Yu Y, Feng W, Yan Q, Gong Y. Host species as a strong determinant of the intestinal microbiota of fish larvae. The Journal of Microbiology. 2012;50:29–37. https://doi.org/10.1007/s12275-012-1340-1
23. Rimoldi S, Antonini M, Gasco L, Moroni F, Terova G. Intestinal microbial communities of rainbow trout (Oncorhynchus mykiss) may be improved by feeding a Hermetia illucens meal/low-fishmeal diet. Fish Physiology and Biochemistry. 2021;47(2):365–380. https://doi.org/10.1007/s10695-020-00918-1
24. Zhao J, Pan J, Zhang Z, Chen Z, Mai K, et al. Fishmeal protein replacement by defatted and full‐fat black soldier fly larvae meal in juvenile turbot diet: Effects on the growth performance and intestinal microbiota. Aquaculture Nutrition. 2023;2023:1–14. https://doi.org/10.1155/2023/8128141
25. Zueva MS, Miroshnikova EP, Arinzhanov AE, Kilyakova YuV. Modern research on the study of the intestinal microbiome in fish. Animal Husbandry and Fodder Production. 2023;106(2):198–213. https://doi.org/10.33284/2658-3135-106-2-198
26. Liu C, Zhao LP, Shen YQ. A systematic review of advances in intestinal microflora of fish. Fish Physiology and Biochemistry. 2021;47:2041–2053. https://doi.org/10.1007/s10695-021-01027-3
27. Medina‐Félix D, Garibay‐Valdez E, Vargas‐Albores F, Martínez‐Porchas M. Fish disease and intestinal microbiota: A close and indivisible relationship. Reviews in Aquaculture. 2023;15(2):820–839. https://doi.org/10.1111/raq.12762
28. Piazzon MC, Naya-Català F, Simó-Mirabet P, Picard-Sánchez A, Roig FJ, et al. Sex, age, and bacteria: How the intestinal microbiota is modulated in a protandrous hermaphrodite fish. Frontiers in Microbiology. 2019;10:2512. https://doi.org/10.3389/fmicb.2019.02512
29. Merrifield DL, Burnard D, Bradley G, Davies S, Baker RTM. Microbial community diversity associated with the intestinal mucosa of farmed rainbow trout (Oncorhynchus mykiss Walbaum). Aquaculture Research. 2009;40:1064–1072. https://doi.org/10.1111/j.1365-2109.2009.02200.x
30. Hamackova J, Kouril J, Kozak P, Stupka Z. Clove oil as an anaesthetic for different freshwater fish species. Bulgarian Journal of Agricultural Science. 2006;12:185–194.
31. Berkeley R, Houlta J, Krieg N, Sneath P, Staley J, et al. The Bergey bacterial detector. In: Houlta J, editor. Moscow: Mir; 1997, 444 p. (In Russ.)
32. Jamal W, Albert MJ, Rotimi VO. Real-time comparative evaluation of bioMerieux VITEK MS versus Bruker Microflex MS, two matrix-assisted laser desorption-ionization time-of-flight mass spectrometry systems, for identification of clinically significant bacteria. BMC Microbiology. 2014;14:289. https://doi.org/10.1186/s12866-014-0289-0
33. Magurran AE. Ecological diversity and its measurement. In: Chernov YuI. Moscow: Mir; 1992, pp. 14–17.
34. Gulamov M. On the question of the dynamics of structural changes in biodiversity. Journal of Science. 2022;(31):3–8.
35. Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, et al. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nature communications. 2022;(13):6978. https://doi.org/10.1038/s41467-022-34557-2
36. Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. Journal of Animal Physiology and Animal Nutrition. 2022;106(2):441–469. https://doi.org/10.1111/jpn.13619
37. Mohseni P, Ghanbarpour R, Jajarmi M, Bagheri M. Molecular and phenotypic characteristics of isolated Escherichia coli from the skin, gills, and intestine of rainbow trout in retail stores of Kerman, Iran. Iranian Journal of Veterinary Research. 2025;26(1):17–23. https://doi.org/10.22099/ijvr.2025.49736.7331
38. Bi B, Yuan Y, Jia D, Jiang W, Yan H, et al. Identification and pathogenicity of emerging fish pathogen Acinetobacter johnsonii from a disease outbreak in rainbow trout (Oncorhynchus mykiss). Aquaculture Research. 2023;2023(1):1–13. https://doi.org/10.1155/2023/1995494
39. Karami AM, Kania PW, Al-Jubury A, Stefanova D, Krych L, et al. Gut microbiota in rainbow trout Oncorhynchus mykiss with different susceptibility to Flavobacterium psychrophilum infection. Aquaculture. 2025;596(Part 1):741841. https://doi.org/10.1016/j.aquaculture.2024.741841
40. Huyben D, Jarau M, Maclnnes J, Stevenson R, Lumsden J. Impact of infection with Flavobacterium psychrophilum and antimicrobial treatment on the intestinal microbiota of Rainbow Trout. Pathogens. 2023;12(3):454. https://doi.org/10.3390/pathogens12030454
41. Donati VL, Madsen L, Middelboe M, Strube ML, Dalsgaard I. The gut microbiota of healthy and Flavobacterium psychrophilum-infected rainbow trout fry is shaped by antibiotics and phage therapies. Frontiers in microbiology. 2022;13. https://doi.org/10.3389/fmicb.2022.771296
42. Aly SM, Eissa AE, Razek NA, EI-Ramlawy AO. The antibacterial activity and immunomodulatory effect of naturally synthesized chitosan and silver nanoparticles against Pseudomonas fluorescence infection in Nile tilapia (Oreochromis niloticus): An in vivo study. Fish & Shellfish Immunology. 2023;135:108628. https://doi.org/10.1016/j.fsi.2023.108628
43. Cao S, Dicksved J, Lundh T, Vidakovic A, Norouzitallab P, et al. A meta‐analysis revealing the technical, environmental, and host‐associated factors that shape the gut microbiota of Atlantic salmon and rainbow trout. Reviews in Aquaculture. 2024;16(4):1603–1620. https://doi.org/10.1111/raq.12913
44. Anka IZ, Webster TU, McLaughlin S, Overland B, Hitchings M, et al. Gut microbiota diversity affects fish behavior and is influenced by host genetics and early rearing conditions. Open Biology. 2025;15(4):240232. https://doi.org/10.1098/rsob.240232




