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Torsabo D, Ishak SD, Noordin NM, Waiho K, Koh ICC, Yazed MA, Abol-Munafi AB. Optimizing reproductive performance in pangasius catfish broodstock: A review of dietary and molecular strategies. Vet Anim Sci 2024; 25:100375. [PMID: 39005967 PMCID: PMC11245938 DOI: 10.1016/j.vas.2024.100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Pangasius catfish, a significant player in the global whitefish market, encounters challenges in aquaculture production sustainability. Quality broodstock maintenance and seed production are impeded by growth, maturation, and fecundity issues. This review investigates the efficacy of strategic nutrient composition and molecular strategies in enhancing broodstock conditions and reproductive performance across various fish species. A notable knowledge gap for Pangasius catfish hampers aquaculture progress. The review assesses nutrient manipulation's impact on reproductive physiology, emphasizing pangasius broodstock. A systematic review analysis following PRISMA guidelines was conducted to identify research trends and hotspots quantitatively, revealing a focus on P. bocourti and fertilization techniques. Addressing this gap, the review offers insights into dietary nutrients manipulation and genetic tool utilization for improved seed production, contributing to pangasius catfish aquaculture sustainability.
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Affiliation(s)
- Donald Torsabo
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Department of Fisheries and Aquaculture, Joseph Sarwuan Tarka University, Makurdi, Makurdi, Benue State, Nigeria
| | - Sairatul Dahlianis Ishak
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Noordiyana Mat Noordin
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity and Conservation, College of Marine Sciences, Beibu Gulf University, Guangxi, China
- Center for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Ivan Chong Chu Koh
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Muhammad Abduh Yazed
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Ambok Bolong Abol-Munafi
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
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Wang J, Zhang J, Shi M, Ma X, Chen S, Zhou Q, Zhu C. Metabolomic analysis revealed the inflammatory and oxidative stress regulation in response to Vibrio infection in Plectropomus leopardus. JOURNAL OF FISH BIOLOGY 2024. [PMID: 39180247 DOI: 10.1111/jfb.15905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/03/2024] [Accepted: 08/02/2024] [Indexed: 08/26/2024]
Abstract
Frequent outbreaks of infectious diseases in aquaculture have led to significant economic losses. The leopard coral grouper (Plectropomus leopardus) often suffers from vibriosis. Improving host immunity presents a superior strategy for disease control, with minimal side effects compared to the use of antibiotics, highlighting the necessity of exploring the mechanisms underlying the fish's response to pathogen infections. Here, we conducted a comparative metabolomic analysis on the livers of the P. leopardus infected with Vibrio harveyi. A total of 1124 differential metabolites (DMs) were identified, with 190, 218, 359, and 353 DMs being identified at 6, 12, 24, and 48 h post-infection (hpi), respectively. Then, based on the time series analysis, we found that the lipid metabolism pathways were modulated in response to the Vibrio infection, with an increase in the quantity of eicosanoids and gycerophospholipids (GPLs), as well as a decrease in the quantity of bile acids (BAs), vitamin D, and sex hormones. Furthermore, 13 enriched pathways involving 31 DMs were identified through KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses. We identified histamine, 15(S)-HpETE, and anandamide in the transient receptor potential (TRP) channels pathway, as well as (7S,8S)-DiHODE, 5S,8R-DiHODE, and 13(S)-HpODE in the linoleic acid (LA) metabolism pathway. The DM levels increased, which may be attributed to inflammation. The DMs in the thyroid hormone synthesis pathway were identified, and the contents of nicotinamide adenine dinucleotide phosphate (NADPH) and glutathione (GSH) decreased, which may be crucial in antioxidants. Our findings highlighted the dynamic adjustments in lipid metabolism and the response to inflammation and oxidative stress during the infection of V. harveyi in P. leopardus. This study not only deepens our understanding of the metabolic underpinnings of fish immune responses but also lays the groundwork for research into functional metabolomics and mechanisms of disease resistance.
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Affiliation(s)
- Jie Wang
- Southern Marine Science and Engineering Guangdong Laboratory, Guangdong Research Centre on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Junwei Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Meng Shi
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xinran Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Qian Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Chunhua Zhu
- Southern Marine Science and Engineering Guangdong Laboratory, Guangdong Research Centre on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Fisheries College, Guangdong Ocean University, Zhanjiang, China
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Shen Y, Aly RSS, Chen T, Jiang H, Liu Y, Wang Y, Chen X. Short time-series expression transcriptome data reveal the gene expression patterns and potential biomarkers of blood infection with LPS and poly (I:C) in mandarin fish (Siniperca chuatsi). FISH & SHELLFISH IMMUNOLOGY 2024; 153:109806. [PMID: 39102971 DOI: 10.1016/j.fsi.2024.109806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/13/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024]
Abstract
Blood transcriptomics has emerged as a vital tool for tracking the immune system and supporting disease diagnosis, prognosis, treatment, and research. The present study was conducted to analyze the gene expression profile and potential biomarker candidates using the whole blood of mandarin fish (Siniperca chuatsi) infected with LPS or poly (I:C) at 0h, 3h, 6h, and 12h. Our data suggest that 310 shared differentially expressed genes (DEGs) were identified among each comparison group after LPS infection, and 137 shared DEGs were identified after poly (I:C) infection. A total of 62 shared DEGs were differentially expressed in all compared groups after LPS or poly (I:C) infection. Pathways analysis for DEGs in all different compared groups showed that cytokine-cytokine receptor interaction was the most enrichment pathway. The expression levels of genes C-X-C chemokine receptor type 2-like (cxcr2), chemokine (C-C motif) receptor 9a (ccr9a), chemokine (C-C motif) receptor 9b (ccr9b), chemokine (C-X-C motif) receptor 4b (cxcr4b), and interleukin 10 receptor alpha (il10ra) were significantly different in all compared groups and most enriched in cytokine-cytokine receptor interaction pathway. The protein-protein interactions analysis among all shared DEGs showed that cxcr4 was the hub gene with the highest degree. The biomarker candidates discovered in this study may, following validation, prove effective as diagnostic tools in monitoring mandarin fish diseases.
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Affiliation(s)
- Yawei Shen
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China; Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA; Observation and Research Station on Water Ecosystem in Danjiangkou Reservoir of Henan Province, Nanyang 474450, China
| | - Rahma Sakina Said Aly
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Tiantian Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Hewei Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yufei Liu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yongxiang Wang
- Huangshan Fisheries Station, Huangshan 245000, Anhui, China
| | - Xiaowu Chen
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China.
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Ivanova L, Rangel-Huerta OD, Tartor H, Dahle MK, Uhlig S, Fæste CK. Metabolomics and Multi-Omics Determination of Potential Plasma Biomarkers in PRV-1-Infected Atlantic Salmon. Metabolites 2024; 14:375. [PMID: 39057698 PMCID: PMC11279234 DOI: 10.3390/metabo14070375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Metabolomic analysis has been explored to search for disease biomarkers in humans for some time. The application to animal species, including fish, however, is still at the beginning. In the present study, we have used targeted and untargeted metabolomics to identify metabolites in the plasma of Atlantic salmon (Salmo salar) challenged with Piscine orthoreovirus (PRV-1), aiming to find metabolites associated with the progression of PRV-1 infection into heart and skeletal muscle inflammation (HSMI). The metabolomes of control and PRV-1-infected salmon were compared at three time points during disease development by employing different biostatistical approaches. Targeted metabolomics resulted in the determination of affected metabolites and metabolic pathways, revealing a substantial impact of PRV-1 infection on lipid homeostasis, especially on several (lyso)phosphatidylcholines, ceramides, and triglycerides. Untargeted metabolomics showed a clear separation of the treatment groups at later study time points, mainly due to effects on lipid metabolism pathways. In a subsequent multi-omics approach, we combined both metabolomics datasets with previously reported proteomics data generated from the same salmon plasma samples. Data processing with DIABLO software resulted in the identification of significant metabolites and proteins that were representative of the HSMI development in the salmon.
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Affiliation(s)
- Lada Ivanova
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway; (O.D.R.-H.); (H.T.); (M.K.D.); (S.U.)
| | | | | | | | | | - Christiane Kruse Fæste
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway; (O.D.R.-H.); (H.T.); (M.K.D.); (S.U.)
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Erfanmanesh A, Beikzadeh B, Khanzadeh M, Alishahi M. Immuno-protective response of Asian seabass (Lates calcarifer) to inactivated vaccines against Streptococcus iniae and Vibrio harveyi. BMC Vet Res 2024; 20:89. [PMID: 38459562 PMCID: PMC10921715 DOI: 10.1186/s12917-024-03935-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND In this study, the protective immunity and immunogenicity of the monovalent and bivalent Streptococcus iniae and Vibrio harveyi vaccine were evaluated in Asian seabass. To analyze immune responses, 1200 Asian seabass with an average weight of 132.6 ± 25.4 g were divided into eight treatments in triplicates (50 fish per tank) as follows: S. iniae immunized by injection (SI), V. harveyi immunized by injection (VI), bivalent S. iniae and V. harveyi (SVI) immunized by injection, S. iniae immunized by immersion (SIM), V. harveyi (VIM) immunized by immersion, bivalent S. iniae and V. harvei (SVIM) immunized by immersion, phosphate-buffered saline (PBS) by injection (PBSI) and control group without vaccine administration (CTRL). Blood and serum samples were taken at the end of the 30th and 60th days. Then the vaccinated groups were challenged with two bacteria (S. iniae) and (V. harveyi) separately and mortality was recorded for 14 days. RESULTS This study reveals that there is no significant difference in the hematological parameters on the 30th and 60th days of the experiment in the vaccine-immunized groups compared to the CTRL group (P > 0.05). Meanwhile, there was no significant difference in the amount of serum albumin level, respiratory burst activity, and serum bactericidal activity in the vaccine-immunized groups compared to the CTRL group on the 30th and 60th days of the experiment (P > 0.05). Total protein on the 60th day (in the VI and SVI groups), globulin on the 30th day (in the VI and SVI groups) and the 60th day (in the VI group) compared to the CTRL and PBSI groups had a significant increase (P < 0.05). Complement activity (in the VI and SVI groups) and lysozyme (in the SI and SVI groups) increased significantly compared to the control group (P < 0.05). Serum antibody titer against S. iniae had a significant increase in the SI, VI, SVI and SVIM groups compared to the CTRL and PBSI groups (P < 0.05). Serum antibody titer against V. harveyi had a significant increase in the groups immunized with the vaccine compared to the CTRL and PBSI groups (P < 0.05). A significant increase in the relative percentage survival (RPS) following challenge with S. iniae in the SVI (86.6%), SI (83.3%,) and VI (73.3%) groups were observed compared to the CTRL (43.3%) and PBSI (40%) groups (P < 0.05). Also, a significant increase in the RPS after challenge with V. harveyi in the SVI group, VI 86.6%, SVI 83.3%, VIM 80% and SVIM 76.6% were observed compared to the CTRL (46.6%) and PBSI (50%) groups (P < 0.05). CONCLUSION Overall, the results demonstrated that the bivalent vaccine of S. iniae and V. harveywas able to produce significant immunogenicity and RPS in Asian seabass.
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Affiliation(s)
- Ahmad Erfanmanesh
- Animal Biological Product Research Group, Academic Center for Education, Culture and Research (ACECR), Tehran Organization, Tehran, Iran
| | - Babak Beikzadeh
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Majid Khanzadeh
- Animal Biological Product Research Group, Academic Center for Education, Culture and Research (ACECR), Tehran Organization, Tehran, Iran.
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Mojtaba Alishahi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
- Centre of Excellence for Warm Water Fish Health and Disease, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Nguyen NH. Genetics and Genomics of Infectious Diseases in Key Aquaculture Species. BIOLOGY 2024; 13:29. [PMID: 38248460 PMCID: PMC10813283 DOI: 10.3390/biology13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.
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Affiliation(s)
- Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Jia R, Hou Y, Feng W, Nomingerel M, Li B, Zhu J. Multi-Omics Analysis to Understand the Effects of Dietary Proanthocyanidins on Antioxidant Capacity, Muscle Nutrients, Lipid Metabolism, and Intestinal Microbiota in Cyprinus carpio. Antioxidants (Basel) 2023; 12:2095. [PMID: 38136215 PMCID: PMC10740959 DOI: 10.3390/antiox12122095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Proanthocyanidins (Pros), a natural polyphenolic compound found in grape seed and other plants, have received significant attention as additives in animal feed. However, the specific mechanism by which Pros affect fish health remains unclear. Therefore, the aim of this study was to investigate the potential effects of dietary Pro on common carp by evaluating biochemical parameters and multi-omics analysis. The results showed that Pro supplementation improved antioxidant capacity and the contents of polyunsaturated fatty acids (n-3 and n-6) and several bioactive compounds. Transcriptomic analysis demonstrated that dietary Pro caused an upregulation of the sphingolipid catabolic process and the lysosome pathway, while simultaneously downregulating intestinal cholesterol absorption and the PPAR signaling pathway in the intestines. Compared to the normal control (NC) group, the Pro group exhibited higher diversity in intestinal microbiota and an increased relative abundance of Cetobacterium and Pirellula. Furthermore, the Pro group had a lower Firmicutes/Bacteroidetes ratio and a decreased relative abundance of potentially pathogenic bacteria. Collectively, dietary Pro improved antioxidant ability, muscle nutrients, and the diversity and composition of intestinal microbiota. The regulation of lipid metabolism and improvement in muscle nutrients were linked with changes in the intestinal microbiota.
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Affiliation(s)
- Rui Jia
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (R.J.); (Y.H.); (W.F.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Yiran Hou
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (R.J.); (Y.H.); (W.F.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Wenrong Feng
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (R.J.); (Y.H.); (W.F.)
| | | | - Bing Li
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (R.J.); (Y.H.); (W.F.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China;
| | - Jian Zhu
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (R.J.); (Y.H.); (W.F.)
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China;
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Young T, Laroche O, Walker SP, Miller MR, Casanovas P, Steiner K, Esmaeili N, Zhao R, Bowman JP, Wilson R, Bridle A, Carter CG, Nowak BF, Alfaro AC, Symonds JE. Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates. BIOLOGY 2023; 12:1135. [PMID: 37627019 PMCID: PMC10452023 DOI: 10.3390/biology12081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | | | | | - Matthew R. Miller
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | | | | | - Noah Esmaeili
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - John P. Bowman
- Tasmanian Institute of Agricultural Research, University of Tasmania, Hobart 7005, Australia
| | - Richard Wilson
- Central Science Laboratory, Research Division, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
- Blue Economy Cooperative Research Centre, Launceston 7250, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
| | - Jane E. Symonds
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
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Natnan ME, Low CF, Chong CM, Bunawan H, Baharum SN. Oleic acid as potential immunostimulant in metabolism pathways of hybrid grouper fingerlings (Epinephelus fuscoguttatus × Epinephelus lanceolatus) infected with Vibrio vulnificus. Sci Rep 2023; 13:12830. [PMID: 37553472 PMCID: PMC10409752 DOI: 10.1038/s41598-023-40096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 08/04/2023] [Indexed: 08/10/2023] Open
Abstract
Grouper culture has been expanding in Malaysia due to the huge demand locally and globally. However, due to infectious diseases such as vibriosis, the fish mortality rate increased, which has affected the production of grouper. Therefore, this study focuses on the metabolic profiling of surviving infected grouper fed with different formulations of fatty acid diets that acted as immunostimulants for the fish to achieve desirable growth and health performance. After a six-week feeding trial and one-week post-bacterial challenge, the surviving infected grouper was sampled for GC-MS analysis. For metabolite extraction, a methanol/chloroform/water (2:2:1.8) extraction method was applied to the immune organs (spleen and liver) of surviving infected grouper. The distribution patterns of metabolites between experimental groups were then analyzed using a metabolomics platform. A total of 50 and 81 metabolites were putatively identified from the spleen and liver samples, respectively. Our further analysis identified glycine, serine, and threonine metabolism, and alanine, aspartate and glutamate metabolism had the most impacted pathways, respectively, in spleen and liver samples from surviving infected grouper. The metabolites that were highly abundant in the spleen found in these pathways were glycine (20.9%), l-threonine (1.0%) and l-serine (0.8%). Meanwhile, in the liver l-glutamine (1.8%) and aspartic acid (0.6%) were found to be highly abundant. Interestingly, among the fish diet groups, grouper fed with oleic acid diet produced more metabolites with a higher percent area compared to the control diets. The results obtained from this study elucidate the use of oleic acid as an immunostimulant in fish feed formulation affects more various immune-related metabolites than other formulated feed diets for vibriosis infected grouper.
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Affiliation(s)
- Maya Erna Natnan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
| | - Chen-Fei Low
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
| | - Chou-Min Chong
- Laboratory of Immunogenomics, Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Hamidun Bunawan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
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Li C, Xing X, Qi H, Liu Y, Jian F, Wang J. The arachidonic acid and its metabolism pathway play important roles for Apostichopus japonicus infected by Vibrio splendens. FISH & SHELLFISH IMMUNOLOGY 2022; 125:152-160. [PMID: 35561951 DOI: 10.1016/j.fsi.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/22/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Improving the immune ability and guiding healthy culture for sea cucumber by purposefully screening the significant differential metabolites when Apostichopus japonicus (A. japonicus) is infected by pathogens is important. In this study, 35 types of significant differential metabolites appeared when A. japonicus were infected by Vibrio splendens (VSI group) compared with the control A. japonicus group (CK group) by using liquid chromatography-mass spectrometry (LC-MS/MS)-based untargeted metabolomics. Based on that finding, the 10 types of key metabolic pathways were analyzed by MetPA. The "arachidonic acid (ARA) metabolism" pathway, which was screened by three elevated biomarkers: ARA, prostaglandin F2α and 2-arachidonoyl glycerol, had an important impact on immune stress in A. japonicus. Due to the similar changes in several metabolites in its metabolic pathway, the ARA metabolic pathway was selected for further study. The activities of ACP, AKP and lysozyme, which are important innate immune-related enzymes, the survival rates of A. japonicus infected with V. splendidus and the relative content of ARA in the body wall detected by GC-MS were all upregulated significantly by exogenous daily 0.60% and 1.09% ARA consumption over a short period of approximately 7 days. These results demonstrated that ARA and its metabolic pathway indeed played important roles in the immunity of A. japonicus infected by the pathogen. The findings also provide novel insights for the effects of metabolites in A. japonicum healthy culture.
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Affiliation(s)
- Cheng Li
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning Province, PR China.
| | - Xuan Xing
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning Province, PR China
| | - Hongqing Qi
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning Province, PR China
| | - Ying Liu
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning Province, PR China
| | - Fanjie Jian
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning Province, PR China
| | - Jihui Wang
- Department of Biotechnology, School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning Province, PR China
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