Mingazova MS, Kilyakova YuV, Miroshnikova EP, Arinzhanov AЕ.

Animal Husbandry and Fodder Production. 2026. Vol. 109. No. 2. Р. 78-95.

doi: 10.33284/2658-3135-109-2-78

 

Original article

Taxonomic profile of the gut microbiota of carp

 

Marina S Mingazova1, Yulia V Kilyakova2, Elena P Miroshnikova3, Azamat Е Arinzhanov4

1,2,3,4Orenburg State University named after VA Bondarenko, Orenburg, Russia

1ms.mingazova@gmail.com, https://orcid.org/0000-0002-2818-1312

2fish-ka06@mail.ru, https://orcid.org/0000-0002-2385-264X

3elenaakva@rambler.ru, https://orcid.org/0000-0003-3804-5151

4arin.azamat@mail.ru, https://orcid.org/0000-0001-6534-7118

 

Abstract. Recently, there has been a growing interest in various feed preparations used in aquaculture due to their beneficial effects on the fish body. Supplements can be used to increase growth, increase survival, and reduce the number of diseases. The study examined feed preparations and their complexes: group I – vanillin, group II – probiotic, group III – vanillin+probiotic, group IV – vanillin+probiotic+trace elements (Zn, I, Cr, Co), group V – vanillin+probiotic+nanoparticles of silicon dioxide (nanoparticles SiO2), group VI – vanillin+trace elements (Zn, I, Cr, Co)+nanoparticles SiO2 and group VII – vanillin+probiotic+trace elements (Zn, I, Cr, Co)+nanoparticles SiO2. The results showed a positive increase in body weight in some experimental groups: I, II, IV, VI and VII, the growth in which differed from the control from 6.8% (P≤0.05) to 10.2% (P≤0.01). Negative dynamics was found in groups III and V. In the intestinal microbiota of carp, 18 phyla were noted in the control and experimental groups, among which typical representatives prevailed – Pseudomonadota, Fusobacteriota and Bacillota. Distinctive results were obtained in the groups where a probiotic was used as a feed preparation. Representatives of lactic acid bacteria Lactococcus appeared in them. In group I, there was a decrease in representatives of the normal intestinal microbiota. In group III, a decrease in the genus Cetobacterium was found. Multiple favorable  changes  were  found in group VII. Significant changes in alpha diversity were noted in groups VI and VII. In the study of beta diversity, no statistically significant differences were found with the control. Thus, the best results were found in group VII, which showed an increase in carp weight of up to 6.8% (P≤0.05) with a positive change in the composition of the intestinal microbiota.

Keywords: aquaculture, carp, microbiome, growth, vanillin, probiotic, ultrafine particles, trace elements

Acknowledgments: the work was carried out with the financial support of a grant for major scientific projects in priority areas of scientific and technical development (No. 075-15-2024-550).

For citation: Mingazova MS, Kilyakova YuV, Miroshnikova EP, Arinzhanov AЕ. Taxonomic profile of the gut microbiota of carp. Animal Husbandry and Fodder Production. 2026;109(2):78-95. (In Russ.).  https://doi.org/10.33284/2658-3135-109-2-78

 

References

  1. Arinzhanova MS, Miroshnikova EP, Arinzhanov AЕ, Kilyakova JV. Biological effect of ultrafine particles of SiO2, probiotic preparation Bifidobiom and a complex of microelements on the body of carp. Animal Husbandry and Fodder Production. 2023b;106(1):48-66. doi: 10.33284/2658-3135-106-1-48
  2. Denisov DB. A Review of Some Criteria for Assessing Biodiversity. Mathematical Research in the Natural Sciences. 2012;8:90-100.
  3. Zueva MS. Modern experience of including biologically active feed additives in the diet of fish (review). Animal Husbandry and Fodder Production. 2022;105(4):146-164. doi: 10.33284/2658-3135-105-4-146
  4. Stepantsova GE, Nizhnikova EV, Nefedova NP, Vorobjov VI, Lempert OT. Effect study of microelements on fiziologo-biochemical indicators of the rainbow trout. Journal of Science and Education of North-West Russia. 2018;4(2):128-135.
  5. Kozubova L, Simonov G, Naumenko P. The effect of cobalt ascorbate on laying hens. Combined feed. 2012;8:95-96.
  6. Mingazova MS, Miroshnikova EP, Arinzhanov AЕ, Kilyakova YuV. Concentration of chemical elements in carp muscle tissue when biologically active substances are included in the diet. Animal Husbandry and Fodder Production. 2023;106(4):18-29. doi: 10.33284/2658-3135-106-4-18
  7. Mingazova MS, Miroshnikova EP, Arinzhanov AЕ, Kilyakova JuV. The carp microbiome when vanillin and ultrafine particles are included in the diet. Agrarian Scientific Journal. 2025;11:88-95. doi: 10.28983/asj.y2025i11pp88-95
  8. Akter S, Jahan N, Rohani F, Akter Y, Shahjahan M. Chromium supplementation in diet enhances growth and feed utilization of striped catfish (Pangasianodon hypophthalmus). Biological Trace Element Research. 2021;199:4811-4819. doi: 10.1007/s12011-021-02608-2
  9. Calcagnile M, Quarta E, Sicuro A, Pecoraro L, Schiavone R, Tredici SM, Talà A, Corallo A, Verri T, Stabili L, Alifano P. Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) intestinal microbiota. Microbial Ecology. 2025;88(1):37. doi: 10.1007/s00248-025-02531-2
  10. Chen CZ, Li P, Wang WB, Li ZH. Response of growth performance, serum biochemical parameters, antioxidant capacity, and digestive enzyme activity to different feeding strategies in common carp (Cyprinus carpio) under high-temperature stress. Aquaculture. 2022;548(1): doi: 10.1016/j.aquaculture.2021.737636
  11. Churilov MN, Prazdnova EV, Rudoy DV. Psychobiotics in aquaculture: harnessing the microbiome-gut-brain axis for stress management and production enhancement in fish. Animals (Basel). 2025;15(18):2726. doi: 10.3390/ani15182726
  12. De Silva C, Nawawi NM, Abd Karim MM, Abd Gani S, Masarudin MJ, Gunasekaran B, Ahmad SA. The mechanistic action of biosynthesised silver nanoparticles and its application in aquaculture and livestock industries. Animals (Basel). 2021;11(7):2097. doi: 10.3390/ani11072097
  13. Diwan AD, Harke SN, Panche AN. Host-microbiome interaction in fish and shellfish: An overview. Fish and Shellfish Immunology Reports. 2023;4:100091. doi: 10.1016/j.fsirep.2023.100091
  14. EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP). Scientific Opinion on the use of cobalt compounds as additives in animal nutrition. EFSA Journal. 2009;7(12):1383. doi: 10.2903/j.efsa.2009.1383
  15. El-Saadony MT, Alagawany M, Patra AK, Kar I, Tiwari R, Dawood MAO, Dhama K, Abdel-Latif HMR. The functionality of probiotics in aquaculture: An overview. Fish & Shellfish Immunology. 2021;117:36-52. doi: 10.1016/j.fsi.2021.07.007
  16. El-Son MAM, Elbahnaswy S, Khormi MA, Aborasain AM, Abdelhaffez HH, Zahran E. Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture. Fish & Shellfish Immunology. 2025;163:110394. doi: 10.1016/j.fsi.2025.110394
  17. Gramm SY, Beketov SV, Kochetkov NI, Klimov VA, Nikiforov-Nikishin AL, Nikiforov-Nikishin DL. Histological changes in the liver, intestines and kidneys of Clarias gariepinus when using feed with chelated compounds. International Journal of Pharmaceutical Research. 2020;12(3):2380-2391. doi: 10.31838/ijpr/2020.12.03.331
  18. Hao K, Wu ZQ, Li DL, Yu XB, Wang GX, Ling F. Effects of dietary administration of Shewanella xiamenensis A-1, Aeromonas veronii A-7, and Bacillus subtilis, single or combined, on the grass carp (Ctenopharyngodon idella) intestinal microbiota. probiotics and antimicrobial proteins. 2017;9(4):386-396. doi: 10.1007/s12602-017-9269-7
  19. Hayes C, Mitchell A, Huerlimann R, Jolly J, Li C, Booth DJ, Ravasi T, Nagelkerken I. Stomach microbiome simplification of a coral reef fish at its novel cold-range edge under climate change. Molecular Ecology. 2025;34(7):e17704. doi: 10.1111/mec.17704
  20. He W, Rahimnejad S, Wang L, Song K, Lu K, Zhang C. Effects of organic acids and essential oils blend on growth, gut microbiota, immune response and disease resistance of Pacific white shrimp (Litopenaeus vannamei) against  Vibrio    Fish  Shellfish  Immunol.  2017;70:164-173. doi: 10.1016/j.fsi.2017.09.007
  21. Hew SY, Tan PY, Zhao K, Tan HY. Enhancing growth and modulation of gut microbiota in red hybrid Tilapia (Oreochromis sp.) with host-associated Leuconostoc lactis as feed additive. Current Microbiology. 2025;82(4):175. doi: 10.1007/s00284-025-04137-w
  22. Klindwort, A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Research. 2013; 41(1):e1. doi: 1093/nar/gks808
  23. Kolygas MN, Bitchava K, Nathanailides C, Athanassopoulou F. Phytochemicals: essential oils and other extracts for disease prevention and growth enhancement in aquaculture: challenges and opportunities. Animals (Basel). 2025;15(18):2653. doi: 10.3390/ani15182653
  24. Liu Y, Sun LJ, Li SH, Chen YX, Wang WR, Jin YG, Zhang I,  Yang F. Residue depletion of sarafloxacin and its impact on the intestinal microbial community in Yellow River carp (Cyprinus carpio haematopterus) following multiple oral administration. Aquaculture Reports. 2026;48:103607. doi: 10.1016/j.aqrep.2026.103607
  25. Maisch NA, Bereswill S, Heimesaat MM. Antibacterial effects of vanilla ingredients provide novel treatment options for infections with multidrug-resistant bacteria - A recent literature review. Eur J Microbiol Immunol (Bp). 2022;12(3):53- doi: 10.1556/1886.2022.00015
  26. Morshed SM, Lee T-H. The role of the microbiome on fish mucosal immunity under changing environments. Fish & Shellfish Immunology. 2023;139:108877. doi: 10.1016/j.fsi.2023.108877
  27. Paralika V, Makridis P. Microbial interactions in rearing systems for marine fish larvae. Microorganisms. 2025;13(3):539. doi: 10.3390/microorganisms13030539
  28. Pisaniello A, Handley KM, White WL, Angert ER, Clements KD. Ontogenetic variation in the gut microbiota of Kyphosus sydneyanus: a comparative analysis. Microbiology Spectrum. 2025;13(12):e0231725. doi: 10.1128/spectrum.02317-25
  29. Qi X, Zhang Y, Zhang Y, Luo F, Song K, Wang G, Ling F. Vitamin B12 produced by Cetobacterium somerae improves host resistance against pathogen infection through strengthening the interactions within gut microbiota. Microbiome. 2023;11(1):135. doi: 10.1186/s40168-023-01574-2
  30. Rebouças JSA, Vieira AO, Rubas EM, Souza DSM, Kulcheski FR, Müller L, de Oliveira VD, Lima JV, Mendonça FW, Rosa RD, Perazzolo LM. Amazonian buriti and pracaxi as potential functional feed additives to improve shrimp immunity and resistance to WSSV. Fish & Shellfish Immunology. 2025;167:110703. doi: 10.1016/j.fsi.2025.110703
  31. Rimoldi S, Gini E, Koch JFA, Iannini F, Brambilla F, Terova G. Effects of hydrolyzed fish protein and autolyzed yeast as substitutes of fishmeal in the gilthead sea bream (Sparus aurata) diet, on fish intestinal microbiome. BMC Vet Res. 2020;16(1):118. doi: 10.1186/s12917-020-02335-1. Erratum in: BMC Vet Res. 2020;16(1):219. doi: 10.1186/s12917-020-02416-1
  32. Sivamani Y, Sajal H, Elayaperumal S. Dysbiosis of microbiome: A risk factor for cancer, metabolic and inflammatory diseases. Microbial Biofilms: Challenges and Advances in Metabolomic Study. 2023:267-288. doi: 10.1016/B978-0-323-95715-1.00011-X
  33. Sumon MAA, Sumon TA,  Hussain MA,  Lee  SJ,  Jang  WJ,  Shari-fuzzaman SM, Brown CL, Lee EW, Hasan MT. Single and multi-strain probiotics supplementation in commercially prominent finfish aquaculture: Review of the current knowledge. Journal of Microbiology and Biotechnology. 2022;32(6):681-698. doi: 10.4014/jmb.2202.02032
  34. Suzuki A, Shirakata C, Anzai H, Sumiyama D, Suzuki M. Vitamin B12 biosynthesis of Cetobacterium ceti isolated from the intestinal content of captive common bottlenose dolphins (Tursiops truncatus). Microbiology. 2022;168(9):001244. doi: 10.1099/mic.0.001244
  35. Tay DD, Kumar VS, Shapawi R, Shah MD, Ahmad HF, Mazlan N. The Relationship between the gut microbiome and the aqua cultured fish, general prospects toward fish health: a systematic review. Applied Biochemistry and Biotechnology. 2025;197(10):6314-6357. doi: 10.1007/s12010-025-05330-0
  36. Ullah S, Feng F, Zhao M, Zhang J, Shao Q. Comparative effects of dietary supplementations with microencapsulated sodium butyrate, glycerol monolaurate and tributyrin on growth, immunity, and gut health in black sea bream. Animals (Basel). 2025;15(6):810. doi: 10.3390/ani15060810
  37. Wang Z, Zhang C, Lu K, Song K, Li X, Wang L, Rahimnejad S. Effects of supplementing intestinal autochthonous bacteria in plant-based diets on growth, nutrient digestibility, and gut health of bullfrogs (Lithobates catesbeianus). Front. Microbiol. 2021;12:739572. doi: 10.3389/fmicb.2021.739572
  38. Wu S, Wang G, Angert ER, Wang W, Li W, Zou H. Composition, diversity, and origin of the bacterial community in grass carp intestine. PloS ONE. 2012;7(2):e30440. doi: 1371/journal.pone.0030440
  39. Xu K, Zhang Y,  Huang  Y,  Wang  Toxicological effects of microplastics and phenanthrene  to  zebrafish  (Danio  rerio).  Science  of  the  Total  Environment. 2021;757:143730. doi: 10.1016/J.SCITOTENV.2020.143730
  40. Yang Q, Jin Y, Yang L, Hu R, Ma J, Wu Z, Yang T, Yang B, Li S, Cong W, Kang Y. Decadal meta-analysis confirms Bacillus spp. optimizes fish intestinal microbiota. Annals of the New York Academy of Sciences. 2026;1556(1):e70154. doi: 10.1111/nyas.70154
  41. Yoon D-S, Kim j-H, Kim I-C, Wang Y, Yang Z, Lee M-C, Lee J-S. Effects of environmental factors on host-microbiota interactions in the guts of aquatic organisms: A review. Comparative Biochemistry and Physiology. Part C: Toxicology & Pharmacology. 2026;300:110381. doi: 10.1016/j.cbpc.2025.110381
  42. Yu J, Zhong D, Li S, Zhang Z, Mo H, Wang L. Acute temperature stresses trigger liver transcriptome and microbial community remodeling in largemouth bass (Micropterus salmoides). Aquaculture. 2023;573(13):739573. doi: 10.1016/j.aquaculture.2023.739573
  43. Yu X-Z, Yu Y, Liu Z-Y. Crosstalk between intestinal microbiota and host defense peptides in fish. Biology (Basel). 2025;14(9):1243. doi: 10.3390/biology14091243
  44. Zaminhan-Hassemer M, Zagolin GB, Aráujo BC, Perazza CA, Barbosa DA, Menegidio FB, Coutinho LL, Tizioto P, Hilsdorf AWS. Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia. Veterinary Research Communications. 2025;49(2):120. doi: 10.1007/s11259-025-10683-2
  45. Zhang L, Liu Z, Deng Y, He C, Liu W, Li X. The benefits of nanosized magnesium oxide in fish Megalobrama amblycephala: evidence in growth performance, redox defense, glucose metabolism, and magnesium homeostasis. Antioxidants (Basel). 2023;12(7):1350. doi: 10.3390/antiox12071350

Information about the authors:

Marina S Mingazova, Cand. Sci. (Biology), Senior Lecturer of the Department of Biotechnology of  Animal  Raw  Materials  and  Aquaculture,  Orenburg State University named after VA Bondarenko, 13 Pobedy Ave, Orenburg, 460018, tel: 8-922-853-24-46.

Yulia V Kilyakova, Cand. Sci. (Biology), Associate Professor, Department of Biotechnology of Animal  Raw  Materials  and  Aquaculture,  Orenburg  State  University  named  after  VA Bondarenko, 13 Pobedy Ave, Orenburg, 460018, tel.: 8-961-920-40-64.

Elena P Miroshnikova, Dr. Sci. (Biology), Professor, Head of the Department of Biotechnology of Animal Raw Materials and Aquaculture, Orenburg State University named after VA Bondarenko, 13 Pobedy Ave, Orenburg, 460018, tel.: 8-987-862-98-86.

Azamat E Arinzhanov, Cand. Sci. (Agriculture), Associate Professor, Department of Biotechnology of Animal Raw Materials and Aquaculture, Orenburg State University named after VA Bondarenko, 13 Pobedy Ave, Orenburg, 460018, tel.: 8-922-806-33-43.

The article was submitted 16.02.2026; approved after reviewing 19.05.2026; accepted for publication 15.06.2026.

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