Intestinal microbiome and immune genes of rolo sturgeon hybrid using probiotics

In sturgeon aquaculture, maintaining a balanced gut microbiome and immune function is critical to maintaining health and improving productivity. The gut microbiome composition and immune genes were studied in hybrid sturgeon after adding probiotics to the feed. Five groups participated in the 14-day experiment: control (feed without additives) and experimental groups receiving probiotics «Ecoflor» and «Florin forte» in different dosages. For the study, the intestines of five individuals were collected before the experiment and in each group on day 14. The microbiome was analyzed using the metabarcoding method of variable regions V3-V4 of the 16S rRNA gene. Immune genes (cytokines, antimicrobial peptides and tight junction proteins) were detected using PCR analysis. It was found that before the experiment, the opportunistic phylum Pseudomonadota dominated in the fish intestine. However, after the use of probiotics, a change in the dominant taxon to Bacillota_D and Bacillota_A, Desulfobacterota_I was noted in all groups. The target probiotic strains Lactobacillus and Bifidobacterium were not detected, probably due to the short duration of the experiment and maintenance conditions. Analysis of the immune status revealed a variable pattern of the presence of the studied genes between the groups. The highest proportion of positive results for immune genes was noted in fish before the experiment and in the group receiving «Ecoflor» at a dosage of 7 g. When studying the correlation matrix, significant relationships were found between the composition of the microbiome and immune genes. It was found that opportunistic Bacillota_D and Bacillota_C negatively affected the immune response and disrupted the integrity of the intestinal barrier. In contrast, Desulfobacterota_I stimulated defense mechanisms, positively correlating with antimicrobial peptides. The use of drugs during the experimental period led to significant but multidirectional changes in the microbiome.

1. Grigoriev V.A., Kulikov M., Mazanko M.S., Prazdnova E.V., Chistyakov V., Rudoy D., Bren A., Kovaleva A.V., Ivanov Yu., Science in the South of Russia, 2024, Vol. 20, No. 1, pp. 70–76, DOI: 10.7868/25000640240109. (In Russ.)

2. Kilyakova Yu.V., Miroshnikova E.P., Arinzhanov A.E., Mingazova M.S., Veterinary pathology, 2024, Vol. 23, No. 4, pp. 52–66, DOI: 10.23947/2949–4826-2024-23-4-52-66 (In Russ.)

3. Kochetkov N.I., Nikiforov-Nikishin D.L., Smorodinskaya S.V., Klimuk A.A., Golovacheva N.A., Fisheries, 2024, No. 4, pp. 96–107, DOI 10.36038/0131-6184-2024-4-96-107. (In Russ.)

4. Malenkina K.A., Arinzhanov A.E., Bulletin of the Orenburg State Agrarian University, 2024, No. 1 (105), pp. 291– 297, DOI: 10.37670/2073-0853-2024-105-1-291-297. (In Russ).

5. Rudoy D.V., Bren’ A.B., Prazdnova E.V., New feed additives in aquaculture: the key to a comprehensive solution to the main problems of the industry, Collection of materials of the XXXII Moscow International Veterinary Congress, Moscow, April 10–12, 2024, Moscow: Publishing house «Scientific Library», 2024, pp. 101–110. (In Russ).

6. Yurin D.A., Maxim E.A., Osepchuk D.V., Danilova A.A., Tletseruk I.R., Collection of scientific papers of the Krasnodar Scientific Center for Animal Science and Veterinary Medicine, 2022, Vol. 11, No. 1, pp. 100–104, DOI: 10.48612/ sbornik-2022-1-23. (In Russ).

7. Arciuch-Rutkowska M., Nowosad J., Łuczyński M.K., Hussain S.M., Kucharczyk D., Next-Generation Sequencing to Determine Changes in the Intestinal Microbiome of Juvenile Sturgeon Hybrid (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) Resulting from Sodium Butyrate, Β-Glucan and Vitamin Supplementation, Genes, 2024, Vol. 15, No. 10, DOI: 10.3390/genes15101276.

8. Maxim E.A., Yurin D.A., Danilova A.A., Tletseruk I.R., Khatkova M.Kh., Bulletin of the Astrakhan State Technical University. Series: Fisheries, 2024, No. 2, pp. 49–56, DOI: 10.24143/2073-5529-2024-2-49-56. (In Russ).

9. Su Q., Peng X., Zhang Z., Xiong Z., He B., Chu P., Zhu C., Isolation, characterization of Bacillus subtilis and Bacillus amyloliquefaciens and validation of the potential probiotic efficacy on growth, immunity, and gut microbiota in hybrid sturgeon (Acipenser baerii ♀ × Acipenser schrenckii ♂), Fish Shellfish Immunol, 2025, Vol. 157, DOI: 10.1016/j.fsi.2024.110081.

10. Wei H.C., Xing S.J., Chen P., Wu X.F., Gu X., Luo L., Liang X.F., Xue M., Plant protein diet-induced hypoimmunity by affecting the spiral valve intestinal microbiota and bile acid enterohepatic circulation in Amur sturgeon (Acipenser schrenckii), Fish Shellfish Immunol, 2020, Vol. 106, pp. 421–430, DOI: 10.1016/j.fsi.2020.08.025.

11. Kurbanov A.R., Degtyarik S.M., Slobodnitskaya G.V., Poloz S.V., Mirolimova Sh.M., Titova N.O., Maksimyuk E.V., Govor T.A., Bespaly A.V., Grebneva E.I., Issues of fisheries of Belarus, 2023, No. 39, pp. 434–453. (In Russ).

12. Sergaliev N.Kh., Andronov E.E., Pinaev A.G., Kakishev M.G., Ginayatov N.S., Collection of scientific papers of the Krasnodar Scientific Center for Animal Science and Veterinary Medicine, 2019, Vol. 8, No. 1, pp. 63–68, DOI: 10.34617/1k2c-7x77. (In Russ).

13. Sergaliev N.Kh., Kakishev M.G., Ginayatov N.S., Andronov E.E., Pinaev A.G., Bulletin of the Izhevsk State Agricultural Academy, 2019, Vol. 2, No. 58, pp. 19–28. (In Russ).

14. Abdul Razak S., Valentine S., Marsh T., Bauman J., Mohd-Assaad N., Scribner K.T., Compositional Dynamics of Gastrointestinal Tract Microbiomes Associated with Dietary Transition and Feeding Cessation in Lake Sturgeon Larvae, Microorganisms, 2022, Vol. 10, No. 9, DOI: 10.3390/microorganisms10091872.

15. Brocca G., Zamparo S., Pretto T., Calore A., Marsella A., Xiccato R.L., Cornaggia M., Cortinovis L., Bano L., Toffan A., Quaglio F., Verin R., Severe gastroenteropathy associated with Clostridium perfringens isolation in starving juvenile sturgeons, J Fish Dis, 2022, Vol. 45, No. 3, pp. 471–477, DOI: 10.1111/jfd.13579.

16. Li Y., Wang R., Zhai C., Cao D., Sun Z., Zhang Y., Ma B., Dynamic Impacts of Stock Enhancement on Kaluga Sturgeon (Huso dauricus): Novel Conservation Strategy Insights from the Gut Microbe Composition and Gene Expression Mode, Int J Mol Sci, 2025, Vol. 26, No. 4, DOI: 10.3390/ijms26041480.

17. Wu X., Teame T., Hao Q., Ding Q., Liu H., Ran C., Yang Y., Zhang Y., Zhou Z., Duan M., Zhang Z., Use of a paraprobiotic and postbiotic feed supplement (HWFTM) improves the growth performance, composition and function of gut microbiota in hybrid sturgeon (Acipenser baerii x Acipenser schrenckii), Fish Shellfish Immunol, 2020, Vol. 104, pp. 36–45, DOI: 10.1016/j.fsi.2020.05.054.

18. Yang S., Xu W., Feng L., Zhang C., Yan C., Zhang J., Lai J., Yan T., He Z., Du X., Du Z., Luo W., Huang X., Wu J., Li Y., Resveratrol Improves the Digestive Ability and the Intestinal Health of Siberian Sturgeon, Int. J. Mol. Sci, 2022, Vol. 23, No. 19.

19. Zarantoniello M., Randazzo B., Nozzi V., Truzzi C., Giorgini E., Cardinaletti G., Freddi L., Ratti S., Girolametti F., Osimani A., Notarstefano V., Milanović V., Riolo P., Isidoro N., Tulli F., Gioacchini G., Olivotto I., Physiological responses of Siberian sturgeon (Acipenser baerii) juveniles fed on full-fat insect-based diet in an aquaponic system, Sci. Rep, 2021, Vol. 11, No. 1, DOI: 10.1038/s41598-020-80379-x.

20. Maxim E.A., Yurina N.A., Yurin D.A., Machneva N.L., Method of growing sturgeon juveniles using probiotics, Bulletin of the Kamchatka State Technical University, 2017, No. 40, pp. 67–76, DOI: 10.17217/2079-0333-2017-40-67-76. (In Russ).

21. Sergaliev N.Kh., Kakishev M.G., Ginayatov N.S., Application of metagenomics methods in assessing the diversity of the microbiome of sturgeons grown in RAS, Veterinary doctor, 2019, No. 5, pp. 38–45, DOI: 10.33632/1998-698X.2019-5-38-45. (In Russ).

22. Soto-Dávila M., Webb R.A., Rodríguez-Ramos T., McDonald G., Effect of dietary supplementation of probiotic on growth, survival, and immune-related biomarkers in Chinook Salmon (Oncorhynchus tshawytscha) challenged with Vibrio anguillarum, Aquaculture, 2024, Vol. 583, DOI: 10.1016/j.aquaculture.2024.740582.

23. Ponomarev S.V., Grozesku Yu.N., Bakhareva A.A., Industrial’noe rybovodstvo (Industrial fish farming), Sanct-Petersburg, 2022, 448 p.

24. Royt A., Brostoff J., Meil D., Immunologiya (Immunology), Moscow: Mir, 2000, 592 p.

25. Mousavi Maleki M.S., Rostamian M., Madanchi H., Antimicrobial peptides and other peptide-like therapeutics as promising candidates to combat SARS-CoV-2, Expert Rev Anti Infect Ther, 2021, Vol. 19, No. 10, pp. 1205–1217, DOI: 10.1080/14787210.2021.1912593.

26. Liu F., Koval M., Ranganathan S., Fanayan S., Hancock W.S., Lundberg E.K., Beavis R.C., Lane L., Duek P., Mc-Quade L., Kelleher N.L., Baker M.S., Systems Proteomics View of the Endogenous Human Claudin Protein Family, J Proteome Res, 2016, Vol. 15, No. 2, pp. 339–359, DOI: 10.1021/acs.jproteome.5b00769.

27. Dörfel M.J., Huber O., Modulation of tight junction structure and function by kinases and phosphatases targeting occluding, J Biomed Biotechnol, 2012, No. 10, DOI: 10.1155/2012/807356.

28. Zhou H., Guan Y., Feng M., Fu Y., Tachibana H., Cheng X., Evaluation on Elongation Factor 1 Alpha of Entamoeba histolytica Interaction with the Intermediate Subunit of the Gal/GalNAc Lectin and Actin in Phagocytosis, Pathogens, 2020, Vol. 9, No. 9, pp. 702, DOI: 10.3390/pathogens9090702.

29. Hintzen J.C.J., Moesgaard L., Kwiatkowski S., Drozak J., Kongsted J., Mecinović J., β-Actin Peptide-Based Inhibitors of Histidine Methyltransferase SETD3, ChemMedChem, 2021, Vol. 16, No. 17, pp. 2695–2702, DOI: 10.1002/cmdc.202100296.

30. Liu X., Li H., Deng H., Zheng C., Yan H., Chen Z., Bian A., Chen J., Zheng K., Glyceraldehyde-3-Phosphate Dehydrogenase of Babesia microti Is a Plasminogen- and Actin-Binding Protein, Front Vet Sci, 2019, No. 6, pp. 228, DOI: 10.3389/fvets.2019.00228.

31. Wang X., Hu G., Wang L., Lu Y., Liu Y., Yang S., Liao J., Zhao Q., Huang Q., Wang W., Guo W., Li H., Fu Y., Song Y., Cai Q., Zhang X., Wang X., Chen Y.Q., Zhang X., Yao H., DEAD-box RNA helicase 10 is required for 18S rRNA maturation by controlling the release of U3 snoRNA from pre-rRNA in embryonic stem cells, Nat Commun, 2024, Vol. 15, No. 1, DOI: 10.1126/sciadv.aba9628.