Metagenomic analysis of the gut microbiome of Nile tilapia (Oreochromis niloticus) from biofloc andpond aquaculture systems in Kerala, South India

Asha Gopan; K. Riji John

doi:10.21077/ijf.2025.72.3.166068-14

Authors

Asha Gopan Kerala University of Fisheries and Ocean Studies
K. Riji John

https://doi.org/10.21077/ijf.2025.72.3.166068-14

Keywords:

Nile tilapia, gut microbiota, biofloc, metagenomics

Abstract

Nile tilapia (Oreochromis niloticus) is one of the most commonly cultured fish species in global aquaculture, with production expected to increase further due to its strong culture performance and resistance to various environmental conditions. The gut microbiota significantly affects the host’s health and the gut of Nile tilapia harbour a diverse microbial community. An experimental study was conducted to analyse the bacterial composition and functional profile of the gut microbiota of Nile tilapia from two different aquaculture systems, Biofloc and Pond culture systems in Kerala, South India. Bacterial communities in the gut of tilapia collected from two systems were classified down to the genus level using 16S rRNA amplicon sequencing. The most prevalent bacterial phyla in the Pond group were Firmicutes, Proteobacteria and Fusobacteria, while Bacteroidetes, Firmicutes and Proteobacteria dominated the biofloc group. At the genus level, Streptococcus and Pseudomonas were the most abundant in the Pond group, whereas Prevotella and Blattobacterium were more prevalent in the Biofloc group. Higher microbial diversity was observed in the gut microbiome of Nile tilapia from the biofloc group. The functional profile of the gut microbiome of Nile tilapia exhibited alterations between the two aquaculture systems. The functional profile of the gut microbiome of Nile tilapia assessed by PiCrust2 revealed that the membrane transport-associated function was predominant in the Pond group and carbohydrate metabolism-associated function in the Biofloc group. The study illustrated how the host environment significantly impacts the composition, diversity and functional profile of the gut microbiome of Nile tilapia.

Keywords: Biofloc, Gut microbiota, Nile tilapia, Metagenomics

Downloads

Download data is not yet available.

Author Biographies

Asha Gopan, Kerala University of Fisheries and Ocean Studies

Department of Aquatic Animal Health

PhD Scholar
K. Riji John

Associate professor, Department of Aquaculture

References

Abdel-Razek, N. 2019. Antimicrobial activities of chitosan nanoparticles against pathogenic microorganisms in Nile tilapia, Oreochromis niloticus. Aquac. Int. 27(5): 1315–1330.

Belkaid, Y. and Hand, T.W. 2014 Role of the microbiota in immunity and inflammation. Cell 157(1), pp.121-141.

Bereded, N. K., Abebe, G. B., Fanta, S. W., Curto, M., Waidbacher, H., Meimberg, H. and Domig, K. J. 2021. The impact of sampling season and catching site (wild and aquaculture) on gut microbiota composition and diversity of Nile tilapia (Oreochromis niloticus). Biol., 10(3): 180.

Bereded, N. K., Curto, M., Domig, K. J., Abebe, G. B., Fanta, S. W., Waidbacher, H. and Meimberg, H. 2020. Metabarcoding analyses of gut microbiota of Nile tilapia (Oreochromis niloticus) from Lake Awassa and Lake Chamo, Ethiopia. Microorganisms, 8(7): 040.

Butt, R. L. and Volkoff, H. 2019. Gut microbiota and energy homeostasis in fish. Front Endocrinol 10: 429202.

Cardona, E., Gueguen, Y., Magré, K., Lorgeoux, B., Piquemal, D., Pierrat, F., Noguier, F. and Saulnier, D. 2016. Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system. BMC Microbiol., 16: 1–9.

Dhariwal, A., Chong, J., Habib, S., King, I.L., Agellon, L.B. and Xia, J. 2017. Microbiome Analyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res., 45(W1), pp.W180-W188.

Dworkin, M. 2006. The prokaryotes: Vol. 5: proteobacteria: alpha and beta subclasses. Springer Science & Business Media.

Emerenciano, M. G. C., Martínez-Córdova, L. R., Martínez-Porchas, M. and Miranda-Baeza, A. 2017. Biofloc technology (BFT): a tool for water quality management in aquaculture. Water Quality, 5: 92-109.

FAO (2022) The State of World Fisheries and Aquaculture 2022: Towards Blue Transformation. https://doi.org/10.4060/cc0461en.

Giatsis, C., Sipkema, D., Smidt, H., Heilig, H., Benvenuti, G., Verreth, J. and Verdegem, M. 2015. The impact of rearing environment on the development of gut microbiota in tilapia larvae. Sci. Rep. 5(1): 18206.

Johny, T. K., Puthusseri, R. M. and Bhat, S. G. 2021. A primer on metagenomics and next‐generation sequencing in fish gut microbiome research. Aquac. Res., 52(10): 4574-4600.

Kaktcham, P. M., Temgoua, J. B., Ngoufack, Z. F., Diaz-Ruiz, G., Wacher, C. and Pérez-Chabela, M. D. L. 2017. Quantitative analyses of the bacterial microbiota of rearing environment, tilapia and common carp cultured in earthen ponds and inhibitory activity of its lactic acid bacteria on fish spoilage and pathogenic bacteria. World J. Microbiol. Biotechnol., 33: 1-12.

Langille, M. G., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R. and Beiko, R.G. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31(9): 814-821

Li, T., Li, H., Gatesoupe, F. J, She, R., Lin, Q., Yan, X., Li, J. and Li, X. 2017. Bacterial signatures of “red-operculum” disease in th.e gut of crucian carp (Carassius auratus). Microb. Ecol. 74: 510-521.

Li, T., Long, M., Ji, C., Shen, Z., Gatesoupe, F. J., Zhang, X., Zhang, Q., Zhang, L., Zhao, Y., Liu, X. and Li, A, 2016. Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis. Sci. Rep. 6(1): 30606.

Mandal, S., Van Treure., W., White, R. A., Eggesbø, M., Knight, R. and Peddada, S. D. 2015. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb. Ecol. Health Dis. 26(1): 27663.

Matsuo, Y., Komiy., S., Yasumizu, Y., Yasuoka, Y., Mizushima, K., Takagi, T., Kryukov, K., Fukuda, A., Morimoto, Y., Naito, Y. and Okada, H. 2021. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. BMC Microbiol. 21:1-13.

McMurtrie, J., Alathari, S., Chaput, D. L., Bass, D., Ghambi, C., Nagoli, J., Delamare-Deboutteville, J., Mohan, C. V., Cable, J., Temperton, B., Tyler, C.R. 2022. Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi. Aquaculture 558: 738367.

Meenakshisundaram., M.., Sugantham, F., Muthukumar, C. and Chandrasekar, M. S. 2021. Metagenomic characterization of biofloc in the grow‐out culture of Genetically Improved Farmed Tilapia (GIFT). Aquac. Res. 52(9): 4249-4262.

Molinari, L. M., Scoaris, D. D. O., Pedroso, R. B., Bittencourt, N. L. R., Nakamura, C. V., Nakamura, T. U., Abreu Filho, B. D. and Dias Filho, B. P. 2003. Bacterial microflora in the gastrointestinal tract of Nile tilapia, Oreochromis niloticus, cultured in a semi-intensive system. Acta Sci. Biol. Sci., 25(2): 267-271.

Mu, L. L., Wu, H. R., Han, K. L., Wu, L. T., Bian, X., Li, B. X., Guo, Z., Yin, X. X. and Ye, J. M. 2019. Molecular and functional characterization of a mannose-binding lectin/ficolin-associated protein (MAp44) from Nile tilapia (Oreochromis niloticus) involved in the immune response to bacterial infection. Dev. Comp. Immunol. 101, UNSP 103438.

Navarrete, P., Magne, F., Araneda, C., Fuentes, P., Barros, L, Opazo, R., Espejo, R. and Romero, J. 2012. PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. PloS One 7(2): 31335.

Pakingking, R., Palma, P. and Usero, R. 2015. Quantitative and qualitative analyses of the bacterial microbiota of tilapia (Oreochromis niloticus) cultured in earthen ponds in the Philippines. World J. Microbiol. Biotechnol. 31: 265-275.

Parshukov, A. N, Kashinskaya, E. N., Simonov, E. P., Hlunov, O. V., Izvekova, G. I., Andree, K. B. and Solovyev, M. M. 2019. Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish. J. Appl. Microbiol. 127(2): 379-395.

Parvatiyar, K., Zhang, Z., Teles, R. M., Ouyang, S., Jiang, Y., Iyer, S. S., Zaver, S. A., Schenk, M., Zeng, S., Zhong, W. and Liu, Z. J. 2012. The helicase DDX41 recognizes the bacterial secondary messengers cyclic di-GMP and cyclic di-AMP to activate a type I interferon immune response. Nat. Immunol. 13(12): 1155-1161.

Precup, G. and Vodnar, D. C. 2019. Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles: a comprehensive literature review. Br. J. Nutr. 122(2): 131-140.

Ray, C. L., Bujan, N., Tarnecki, A. M., Davis, A. D., Browdy, C. L. and Arias, C. R. 2017. Analysis of the gut microbiome of Nile tilapia Oreochromis niloticus L. fed diets supplemented with Previda® and Saponin. J. Fish.Com 11(2): 36.

Sullam, K. E., Essinger, S. D., Lozupone, C. A., O’Connor, M. P., Rosen., G. L., Knight, R. O. B., Kilham, S. S. and Russell, J. A. 2012. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysis. Mol. Ecol. 21(13): 3363-3378.

Summerfelt, R. C. 2000. Water quality considerations for aquaculture. Department of Animal Ecology, pp.2-7.

Tan, C. K., Natrah, I., Suyub, I. B., Edward, M. J., Kaman, N and Samsudin, A. A. 2019. Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides). Microbiology Open 8(5): 00734.

Tran, N. T., Zhang, J., Xiong, F., Wang, G. T., Li, W. X. and Wu, S. G. 2018. Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus). World J. Microbiol. Biotechnol. 34: 1-9.

Wang., J.., Huang, Y., Xu, K., Zhang, X., Sun, H., Fan, L. and Yan, M. 2019. White spot syndrome virus (WSSV) infection impacts intestinal microbiota composition and function in Litopenaeus vannamei. Fish Shellfish Immunol., 84: 130-137

Webster, A. J. F. 1980. Energy costs of digestion and metabolism in the gut. In Digestive Physiology and Metabolism in Ruminants: Proceedings of the 5th International Symposium on Ruminant Physiology, held at Clermont—Ferrand, on 3rd–7th September, 1979 (pp. 469-484). Springer Netherlands.

Wu, Z., Wang, S., Zhang, Q., Hao, J., Lin, Y., Zhang, J. and Li, A. 2020. Assessing the intestinal bacterial community of farmed Nile tilapia (Oreochromis niloticus) by high-throughput absolute abundance quantification. Aquaculture 529: 735688.

Xiao, F., Liao, L., Xu, Q., He, Z., Xiao, T., Wang, J., Huang, J., Yu, Y., Wu, B. and Yan, Q. 2021. Host–microbiota interactions and responses to grass carp reovirus infection in Ctenopharyngodon idellus. Environ. Microbiol. 23(1): 431-447.