Mini-review: Development of High-throughput Omics Resources for Aquaculture Nutrition
Palabras clave:
Aquaculture Nutrition, Omics, Advanced functional feeds, Metabolic pathways, BiomarkersResumen
Enhanced growth, immunity, and resilience are highly sought-after phenotypic traits in aquaculture. In current practice, feeds are purposefully formulated to include ingredients that promote these traits while striving for low production costs, complying with sustainability, and more recently, social license. The use of omics technologies in aquaculture has significantly increased in the last decade with transcriptomics being the most commonly employed tool to infer animal responses to diet or disease challenge. However, by combining transcriptomics with proteomics and metabolomics, it is now plausible to evolve aquaculture nutrition from the viewpoints of enhanced growth and survival to the development of premium advanced functional feeds that help to attain all desired phenotypes. Close proximity of proteins and metabolites to the desired phenotype makes proteomics and metabolomics coupled to bioinformatics a powerful trinomial tool to elucidate functional perturbations in an organism under specific circumstances at a given time. Collectively, omics technologies have unveiled new knowledge regarding specific biomarkers and metabolic pathways associated with specific dietary components or disease challenges across several aquaculture research domains and contributed to defining the future of sustainable aquaculture.
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Addis, M. F., Cappuccinelli, R., Tedde, V., Pagnozzi, D., Porcu, M. C., Bonaglini, E., Roggio, T., & Uzzau, S. (2010). Proteomic analysis of muscle tissue from gilthead sea bream (Sparus aurata, L.) farmed in offshore floating cages. Aquaculture, 309(1), 245-252. doi:https://doi.org/10.1016/j.aquaculture.2010.08.022
Alfaro, A. C., Nguyen, T. V., Rodríguez, J. A., Bayot, B., Domínguez-Borbor, C., Sonnenholzner, S., Azizan, A., & Venter, L. (2022). Evaluation of immune stimulatory products for whiteleg shrimp (Penaeus vannamei) by a metabolomics approach. Fish & Shellfish Immunology, 120, 421-428. doi:https://doi.org/10.1016/j.fsi.2021.12.007
Byelashov, O. A., & Griffin, M. E. (2014). Fish in, fish out: perception of sustainability and contribution to public health. Fisheries, 39(11), 531-535. doi:https://doi.org/10.1080/03632415.2014.967765
Carrera, M., Piñeiro, C., & Martinez, I. (2020). Proteomic strategies to evaluate the impact of farming conditions on food quality and safety in aquaculture products. Foods (Basel, Switzerland), 9(8), 1050. doi:10.3390/foods9081050
Chen, K., Li, E., Xu, C., Wang, X., Li, H., Qin, J. G., & Chen, L. (2019). Growth and metabolomic responses of Pacific white shrimp (Litopenaeus vannamei) to different dietary fatty acid sources and salinity levels. Aquaculture, 499, 329-340. doi:https://doi.org/10.1016/j.aquaculture.2018.09.056
Chen, Y., Chi, S., Zhang, S., Dong, X., Yang, Q., Liu, H., Tan, B., & Xie, S. (2021). Effect of black soldier fly (Hermetia illucens) larvae meal on lipid and glucose metabolism of Pacific white shrimp Litopenaeus vannamei. British Journal of Nutrition, 1-15. doi:10.1017/S0007114521004670
Colgrave, M. L., Goswami, H., Blundell, M., Howitt, C. A., & Tanner, G. J. (2014). Using mass spectrometry to detect hydrolysed gluten in beer that is responsible for false negatives by ELISA. Journal of Chromatography A, 1370, 105-114. doi:https://doi.org/10.1016/j.chroma.2014.10.033
Dai, T., Jiao, L., Tao, X., Lu, J., Jin, M., Sun, P., & Zhou, Q. (2021). Effects of dietary vitamin D3 supplementation on the growth performance, tissue Ca and P concentrations, antioxidant capacitiy, immune response and lipid metabolism in Litopenaeus vannamei larvae. British Journal of Nutrition, 1-20. doi:10.1017/S0007114521004931
Deborde, C., Hounoum, B. M., Moing, A., Maucourt, M., Jacob, D., Corraze, G., Médale, F., & Fauconneau, B. (2021). Putative imbalanced amino acid metabolism in rainbow trout long term fed a plant-based diet as revealed by 1H-NMR metabolomics. Journal of Nutritional Science, 10, e13. doi:10.1017/jns.2021.3
Dettmer, K., Aronov, P. A., & Hammock, B. D. (2007). Mass spectrometry-based metabolomics. Mass Spectrometry Reviews, 26(1), 51-78. doi:https://doi.org/10.1002/mas.20108
Djordjevic, B., Morales-Lange, B., Øverland, M., Mercado, L., & Lagos, L. (2021). Immune and proteomic responses to the soybean meal diet in skin and intestine mucus of Atlantic salmon (Salmo salar L.). Aquaculture Nutrition, 27(4), 929-940. doi:https://doi.org/10.1111/anu.13248
Donaldson, A. E., & Lamont, I. L. (2013). Biochemistry changes that occur after death: potential markers for determining post-mortem interval. PLOS ONE, 8(11), e82011. doi:10.1371/journal.pone.0082011
El-Saadony, M. T., Alagawany, M., Patra, A. K., Kar, I., Tiwari, R., Dawood, M. A. O., Dhama, K., & Abdel-Latif, H. M. R. (2021). The functionality of probiotics in aquaculture: An overview. Fish & Shellfish Immunology, 117, 36-52. doi:https://doi.org/10.1016/j.fsi.2021.07.007
Encarnação, P. (2016). 5 - Functional feed additives in aquaculture feeds. In S. F. Nates (Ed.), Aquafeed Formulation (pp. 217-237). San Diego: Academic Press.
Estruch, G., Martínez-Llorens, S., Tomás-Vidal, A., Monge-Ortiz, R., Jover-Cerdá, M., Brown, P. B., & Peñaranda, D. S. (2020). Impact of high dietary plant protein with or without marine ingredients in gut mucosa proteome of gilthead seabream (Sparus aurata, L.). Journal of Proteomics, 216, 103672. doi:https://doi.org/10.1016/j.jprot.2020.103672
FAO. (2018). The State of World Fisheries and Aquaculture 2018 - Meeting the sustainable development goals. Rome.
Ghaedi, G., Keyvanshokooh, S., Mohammadi Azarm, H., & Akhlaghi, M. (2016). Proteomic analysis of muscle tissue from rainbow trout (Oncorhynchus mykiss) fed dietary β-glucan. Iranian journal of veterinary research, 17(3), 184-189.
Glencross, B., Irvin, S., Arnold, S., Blyth, D., Bourne, N., & Preston, N. (2014). Effective use of microbial biomass products to facilitate the complete replacement of fishery resources in diets for the black tiger shrimp, Penaeus monodon. Aquaculture, 431, 12-19. doi:https://doi.org/10.1016/j.aquaculture.2014.02.033
Glencross, B. D. (2020). A feed is still only as good as its ingredients: An update on the nutritional research strategies for the optimal evaluation of ingredients for aquaculture feeds. Aquaculture Nutrition, 26(6), 1871-1883. doi:https://doi.org/10.1111/anu.13138
Grandiosa, R., Mérien, F., Young, T., Van Nguyen, T., Gutierrez, N., Kitundu, E., & Alfaro, A. C. (2018). Multi-strain probiotics enhance immune responsiveness and alters metabolic profiles in the New Zealand black-footed abalone (Haliotis iris). Fish & Shellfish Immunology, 82, 330-338. doi:https://doi.org/10.1016/j.fsi.2018.08.034
Grandiosa, R., Young, T., Van Nguyen, T., Mérien, F., & Alfaro, A. C. (2020). Immune response in probiotic-fed New Zealand black-footed abalone (Haliotis iris) under Vibrio splendidus challenge. Fish & Shellfish Immunology, 104, 633-639. doi:https://doi.org/10.1016/j.fsi.2020.06.007
Gyawali, P., Karpe, A. V., Hillyer, K. E., Nguyen, T. V., Hewitt, J., & Beale, D. J. (2021). A multi-platform metabolomics approach to identify possible biomarkers for human faecal contamination in Greenshell™ mussels (Perna canaliculus). Science of The Total Environment, 771, 145363. doi:https://doi.org/10.1016/j.scitotenv.2021.145363
Hua, K., Cobcroft, J. M., Cole, A., Condon, K., Jerry, D. R., Mangott, A., Praeger, C., Vucko, M. J., Zeng, C., Zenger, K., & Strugnell, J. M. (2019). The future of aquatic protein: implications for protein sources in aquaculture diets. One Earth, 1(3), 316-329. doi:https://doi.org/10.1016/j.oneear.2019.10.018
Hunter, M. C., Smith, R. G., Schipanski, M. E., Atwood, L. W., & Mortensen, D. A. (2017). Agriculture in 2050: recalibrating targets for sustainable intensification. BioScience, 67(4), 386-391. doi:10.1093/biosci/bix010
Jasour, M. S., Wagner, L., Sundekilde, U. K., Larsen, B. K., Greco, I., Orlien, V., Olsen, K., Rasmussen, H. T., Hjermitslev, N. H., Hammershøj, M., Dalsgaard, A. J. T., & Dalsgaard, T. K. (2017). A comprehensive approach to assess feathermeal as an alternative protein source in aquafeed. Journal of Agricultural and Food Chemistry, 65(48), 10673-10684. doi:10.1021/acs.jafc.7b04201
Jasour, M. S., Wagner, L., Sundekilde, U. K., Larsen, B. K., Rasmussen, H. T., Hjermitslev, N. H., Hammershøj, M., Dalsgaard, A. J. T., & Dalsgaard, T. K. (2018). Fishmeal with different levels of biogenic amines in aquafeed: comparison of feed protein quality, fish growth performance, and metabolism. Aquaculture, 488, 80-89. doi:https://doi.org/10.1016/j.aquaculture.2018.01.030
Knipe, H., Temperton, B., Lange, A., Bass, D., & Tyler, C. R. (2021). Probiotics and competitive exclusion of pathogens in shrimp aquaculture. Reviews in Aquaculture, 13(1), 324-352. doi:https://doi.org/10.1111/raq.12477
Liu, L., Cai, X., Ai, Y., Li, J., Long, H., Ren, W., Huang, A., Zhang, X., & Xie, Z.-y. (2022). Effects of Lactobacillus pentosus combined with Arthrospira platensis on the growth performance, immune response, and intestinal microbiota of Litopenaeus vannamei. Fish & Shellfish Immunology, 120, 345-352. doi:https://doi.org/10.1016/j.fsi.2021.12.005
Lulijwa, R., Alfaro, A. C., & Young, T. (2021). Metabolomics in salmonid aquaculture research: applications and future perspectives. Reviews in Aquaculture, n/a(n/a). doi:https://doi.org/10.1111/raq.12612
Luo, K., Li, J., Chen, J., Pan, Y., Zhang, Y., Zhou, H., Zhang, W., & Mai, K. (2020). Proteomics analysis of skin coloration of large yellow croaker Larimichthys crocea fed different dietary carotenoids. Aquaculture Nutrition, 26(6), 1981-1993. doi:https://doi.org/10.1111/anu.13140
Ma, S., Wang, X., Gao, W., Xu, W., Zhang, W., & Mai, K. (2020). Effects of yeast autolysate in the practical diet on the growth performance, immune response, and disease resistance of Pacific white shrimp. Journal of Aquatic Animal Health, 32(3), 109-115. doi:https://doi.org/10.1002/aah.10095
Martin, S. A. M., Vilhelmsson, O., Médale, F., Watt, P., Kaushik, S., & Houlihan, D. F. (2003). Proteomic sensitivity to dietary manipulations in rainbow trout. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1651(1), 17-29. doi:https://doi.org/10.1016/S1570-9639(03)00231-0
Mendoza-Porras, O., Botwright, N. A., McWilliam, S. M., Cook, M. T., Harris, J. O., Wijffels, G., & Colgrave, M. L. (2014). Exploiting genomic data to identify proteins involved in abalone reproduction. Journal of Proteomics, 108, 337-353. doi:https://doi.org/10.1016/j.jprot.2014.06.001
Mendoza-Porras, O., Botwright, N. A., Reverter, A., Cook, M. T., Harris, J. O., Wijffels, G., & Colgrave, M. L. (2017). Identification of differentially expressed reproductive and metabolic proteins in the female abalone (Haliotis laevigata) gonad following artificial induction of spawning. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 24, 127-138. doi:https://doi.org/10.1016/j.cbd.2016.04.005
Mendoza-Porras, O., Harris, J. O., Wijffels, G., Reverter, A., Cook, M. T., Botwright, N. A., & Colgrave, M. L. (2017). Gonadal reproductive and metabolic proteins of male abalone Haliotis laevigata (Donovan, 1808) assessed by targeted mass spectrometry after artificial induction of spawning. Aquaculture Research, 48(12), 6009-6015. doi:https://doi.org/10.1111/are.13413
Mendoza-Porras, O., Kamath, S., Harris, J. O., Colgrave, M. L., Huerlimann, R., Lopata, A. L., & Wade, N. M. (2020). Resolving hemocyanin isoform complexity in haemolymph of black tiger shrimp Penaeus monodon - implications in aquaculture, medicine and food safety. Journal of Proteomics, 218, 103689. doi:https://doi.org/10.1016/j.jprot.2020.103689
Morais, S., Silva, T., Cordeiro, O., Rodrigues, P., Guy, D. R., Bron, J. E., Taggart, J. B., Bell, J. G., & Tocher, D. R. (2012). Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar). BMC Genomics, 13(1), 448. doi:10.1186/1471-2164-13-448
Mustafa, S. A., & Al-Faragi, J. K. (2021). Supplementation of feed additives on aquaculture feeds: a review. International Journal of Pharmaceutical Research, 13(1).
Neuheimer, A. B., Thresher, R. E., Lyle, J. M., & Semmens, J. M. (2011). Tolerance limit for fish growth exceeded by warming waters. Nature Climate Change, 1(2), 110-113. doi:10.1038/nclimate1084
Nguyen, T. V., Alfaro, A., Arroyo, B. B., Leon, J. A. R., & Sonnenholzner, S. (2021). Metabolic responses of penaeid shrimp to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. Aquaculture, 533, 736174. doi:https://doi.org/10.1016/j.aquaculture.2020.736174
Nguyen, T. V., Alfaro, A. C., Mundy, C., Petersen, J., & Ragg, N. L. C. (2022). Omics research on abalone (Haliotis spp.): Current state and perspectives. Aquaculture, 547, 737438. doi:https://doi.org/10.1016/j.aquaculture.2021.737438
Nissa, M. U., Pinto, N., Mukherjee, A., Reddy, P. J., Ghosh, B., Sun, Z., Ghantasala, S., Chetanya, C., Shenoy, S. V., Moritz, R. L., Goswami, M., & Srivastava, S. (2021). Organ-based proteome and post-translational modification profiling of a widely cultivated tropical water fish, Labeo rohita. Journal of Proteome Research. doi:10.1021/acs.jproteome.1c00759
Nissa, M. U., Pinto, N., Parkar, H., Goswami, M., & Srivastava, S. (2021). Proteomics in fisheries and aquaculture: an approach for food security. Food Control, 127, 108125. doi:https://doi.org/10.1016/j.foodcont.2021.108125
Noble, T. H., Rao, M., Briggs, M., Shinn, A. P., Simon, C., & Wynne, J. W. (2021). Novacq™ improves survival of Penaeus vannamei when challenged with pathogenic Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease. Aquaculture, 545, 737235. doi:https://doi.org/10.1016/j.aquaculture.2021.737235
Nuez-Ortín, W. G., Carter, C. G., Nichols, P. D., Cooke, I. R., & Wilson, R. (2018). Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature. BMC Genomics, 19(1), 133. doi:10.1186/s12864-018-4517-0
Raposo de Magalhães, C., Schrama, D., Farinha, A. P., Revets, D., Kuehn, A., Planchon, S., Rodrigues, P. M., & Cerqueira, M. (2020). Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare research. BMC Genomics, 21(1), 309. doi:10.1186/s12864-020-6728-4
Rombenso, A. N., Duong, M. H., Hines, B. M., Mã, T., & Simon, C. J. (2021). The marine microbial biomass, Novacq™, a useful feed additive for postlarvae and juvenile Litopenaeus vannamei. Aquaculture, 530, 735959. doi:https://doi.org/10.1016/j.aquaculture.2020.735959
Roques, S., Deborde, C., Richard, N., Skiba-Cassy, S., Moing, A., & Fauconneau, B. (2020). Metabolomics and fish nutrition: a review in the context of sustainable feed development. Reviews in Aquaculture, 12(1), 261-282. doi:https://doi.org/10.1111/raq.12316
Sellars, M. J., Rao, M., Polymeris, N., Irvin, S. J., Cowley, J. A., Preston, N. P., & Glencross, B. D. (2015). Feed containing novacq improves resilience of black tiger shrimp, Penaeus monodon, to gill-associated virus-induced mortality. Journal of the World Aquaculture Society, 46(3), 328-336. doi:https://doi.org/10.1111/jwas.12190
Timmins-Schiffman, E. B., Crandall, G. A., Vadopalas, B., Riffle, M. E., Nunn, B. L., & Roberts, S. B. (2017). Integrating discovery-driven proteomics and selected reaction monitoring to develop a noninvasive assay for geoduck reproductive maturation. Journal of Proteome Research, 16(9), 3298-3309. doi:10.1021/acs.jproteome.7b00288
Tripathy, P. S., Khatei, A., & Parhi, J. (2021). Omics in aquaculture. In P. K. Pandey & J. Parhi (Eds.), Advances in Fisheries Biotechnology (pp. 83-94). Singapore: Springer Singapore.
Turchini, G. M., Trushenski, J. T., & Glencross, B. D. (2019). Thoughts for the future of aquaculture nutrition: realigning perspectives to reflect contemporary issues related to judicious use of marine resources in aquafeeds. North American Journal of Aquaculture, 81(1), 13-39. doi:https://doi.org/10.1002/naaq.10067
Wade, N. M., Clark, T. D., Maynard, B. T., Atherton, S., Wilkinson, R. J., Smullen, R. P., & Taylor, R. S. (2019). Effects of an unprecedented summer heatwave on the growth performance, flesh colour and plasma biochemistry of marine cage-farmed Atlantic salmon (Salmo salar). Journal of Thermal Biology, 80, 64-74. doi:https://doi.org/10.1016/j.jtherbio.2018.12.021
Wagner, L., Gómez-Requeni, P., Moazzami, A. A., Lundh, T., Vidakovic, A., Langeland, M., Kiessling, A., & Pickova, J. (2019). 1H NMR-based metabolomics and lipid analyses revealed the effect of dietary replacement of microbial extracts or mussel meal with fish meal to Arctic charr (Salvelinus alpinus). Fishes, 4(3), 46.
Wagner, L., Trattner, S., Pickova, J., Gómez-Requeni, P., & Moazzami, A. A. (2014). 1H NMR-based metabolomics studies on the effect of sesamin in Atlantic salmon (Salmo salar). Food Chemistry, 147, 98-105. doi:https://doi.org/10.1016/j.foodchem.2013.09.128
Wang, J., Janech, M. G., & Burnett, K. G. (2019). Protein-level evidence of novel β-type hemocyanin and heterogeneous subunit usage in the pacific whiteleg shrimp, Litopenaeus vannamei. Frontiers in Marine Science, 6. doi:10.3389/fmars.2019.00687
Xu, Z.-N., Zheng, G.-D., Wu, C.-B., Jiang, X.-Y., & Zou, S.-M. (2019). Identification of proteins differentially expressed in the gills of grass carp (Ctenopharyngodon idella) after hypoxic stress by two-dimensional gel electrophoresis analysis. Fish Physiology and Biochemistry, 45(2), 743-752. doi:10.1007/s10695-018-0599-5
