An Overview of Advancements in Proteomic Approaches to Enhance Livestock Production and Aquaculture
Simple Summary
Abstract
1. Introduction
2. Applications of Proteomics in Livestock Production
2.1. Genetic Improvement and Breeding Programs
2.2. Feed Efficiency and Nutritional Optimization
2.3. Stress and Welfare
Indicators | Proteomics Techniques/Method | Species | Findings | References |
---|---|---|---|---|
Stress response | LC-MS/MS | Swine | Label-free quantitative proteomics identified 66 differentially abundant proteins between non-stressed and stressed pigs, with 30 increased and 36 decreased in the non-stressed group. | [67] |
Pre-slaughter stress | OFFGEL, SDS-PAGE and LC-MS | Bovine | Five protein bands showed significant differences between normal and DFD meat samples, containing actin, phosphoglucomutase-1, alpha-crystallin B, heat shock protein beta-6, and heat shock protein beta-1. | [68] |
Chronic lameness | LC-MS/MS and SDS-PAGE | Bovine | Chronic inflammatory lameness in dairy cows is associated with increased expression of stress proteins with chaperone, metabolism, redox, and structural functions in the dorsal horn of the spinal cord. | [69] |
Heat stress | LC-MS/MS | Swine | Overexpression of HSP70 in intestinal epithelial cells led to changes in the expression of many proteins involved in cell–extracellular matrix interactions, cell adhesion, and apoptosis. | [70] |
Environmental enrichment | iTRAQ and LC-MS/MS | Swine | Pigs in enriched environments had lower plasma cortisol and lactate levels, indicating a reduced stress response. Pigs in enriched environments showed changes in neurotransmitter levels in the brain, including decreased noradrenaline and dopamine, and increased serotonin, also suggesting a lower stress response. | [71] |
Slaughter methods | MALDI-TOF MS | Poultry | Ritual slaughter without stunning resulted in significantly elevated stress indicators like cortisol and triiodothyronine compared to commercial slaughter with electrical stunning. | [72] |
Electrical stunning | 2-DE and MALDI-TOF/TOF MS | Sheep | The study found 243 proteins that were significantly differentially expressed between stunned and non-stunned (halal) slaughter, with 119 being upregulated and 124 being downregulated. | [73] |
Chronic circadian disruption | LC-MS/MS | Bovine | Dairy cows exposed to circadian rhythm disruption during late gestation showed increased markers of oxidative stress and metabolism in their muscle tissue. | [74] |
Response of bovine granulosa cells to acute heat stress | LC-MS/MS | Bovine | Heat stress triggered oxidative stress-mediated apoptosis in bovine granulosa cells (bGCs), but the cells exhibited a time-dependent recovery of proliferation potential by 48 h. The study identified 37 differentially regulated metabolites in bGCs in response to acute heat stress, which were involved in bioenergetics support mechanisms and cellular adaptations. | [75] |
2.4. Disease Diagnosis and Health Management
Indicators | Proteomics Techniques/Method | Species | Findings | References |
---|---|---|---|---|
Neosporosis | LC-MS/MS | Bovine | Neospora caninum infection primarily impacts the host cell’s mitochondrial processes and metabolism. The low-virulence isolate Nc-Spain1H had a greater influence on the host cell proteome compared to the high-virulence isolate Nc-Spain7. | [92] |
Salmonella infection | LC-MS/MS | Poultry | Salmonella infection increased the abundance of proteins involved in the host’s response to oxidative stress, amino acid metabolism, and lysosomal activity in the spleen of broiler chickens. Salmonella infection decreased the abundance of proteins involved in cell cycle progression, RNA binding, and cytoskeletal development in the spleen of broiler chickens. | [93] |
Pneumonia and mastitis | 2-DE and MALDI-TOF mass spectrometry | Bovine | Identified 60 secreted proteins from Mycoplasma bovis, a pathogen that causes pneumonia and mastitis in cattle, and 8 of these proteins were predicted to be virulence-related factors. | [94] |
Mycobacterium avium paratuberculosis infection | label-free LC-MS/MS | Bovine | Cows resistant to MAP infection showed higher abundance of TLR2 and MHC class II proteins in their PBMCs, indicating a successful defensive immune response. Cows persistently infected with MAP showed higher abundance of ITGA2B and KCNMA1 in their PBMCs, suggesting an unsuccessful immune response. | [95] |
Ketosis | LC-MS | Bovine | The metabolomic analysis showed that cows with clinical ketosis had significant alterations in pathways related to amino acid, carbohydrate, and nucleotide metabolism compared to healthy controls, and these changes were consistent across the transition from prepartum to postpartum. | [96] |
Toxoplasma gondii infection | iTRAQ labeling, and LC-MS/MS | Pig | Overexpression of two potential anti-T. gondii proteins, HSP70.2 and PDIA3, in swine macrophage cells enhanced resistance to T. gondii infection. | [97] |
Mastitis | MALDI-TOF mass spectrometry | Goat | Identified the Staphylococcus species present in 19 isolates from subclinical caprine mastitis, with S. epidermidis being the most common at 47.36%. Henotypic resistance testing showed high resistance to penicillin G (58%), but lower resistance to cefoxitin and oxacillin (both 26.31%). All strains were susceptible to amoxicillin + clavulanic acid. | [98] |
Coinfection with Marek’s disease virus and reticuloendotheliosis virus | Tandem mass tag (TMT) labeling and LC-MS/MS | Chicken | MDV and REV coinfection increased viral replication compared to single infections. Coinfection led to differential expression of 98 proteins, with 38 upregulated and 60 downregulated. | [99] |
Rotavirus infection | iTRAQ and LC-MS/MS | Pig | Identified 223 differentially accumulated proteins (DAPs) in porcine rotavirus (PoRV)-infected IPEC-J2 cells compared to mock-infected cells, with 125 being up-accumulated and 98 being down-accumulated. | [100] |
Deltacoronavirus | iTRAQ and LC-MS/MS | Pig | A total of 78 differentially expressed proteins (DEPs) were identified in IPEC-J2 cells infected with porcine deltacoronavirus (PDCoV), with 23 being upregulated and 55 being downregulated. | [101] |
Mastitis | MALDI-TOF MS | Bovine | MALDI-TOF MS fingerprinting was superior to 16S rRNA gene sequencing for discriminating between different streptococcal species and subspecies involved in bovine mastitis. MALDI-TOF MS analysis identified three specific protein biomarkers characteristic of the Streptococcus genus and showed variability at both the species and subspecies level. | [102] |
3. Applications of Proteomics in Aquaculture
3.1. Proteomic Insights into Fish Physiology
Indicators | Technique Used | Species | Findings | References |
---|---|---|---|---|
Immune and stress biomarkers in skin mucus | 2D-PAGE, LC-MS/MS | Gadus morhua, Cyclopterus lumpus | Identified immune-related proteins such as galectin-1, cystatin B, heat shock proteins, and peroxiredoxin1. | [106,110] |
Innate immunity and physiological status | LC-MS/MS, 2-DE | Sparus aurata | Key proteins (e.g., actins, glycolytic enzymes, heat shock proteins) linked to immune defense, metabolism, and stress responses. | [111,112] |
Antimicrobial and proteolytic activity | Nano-LC-MS/MS | Scorpaena plumieri | Identified 391 proteins with antimicrobial and venom-related activity, including proteolytic enzymes. | [113] |
Feeding mechanisms of bloodsucking fish | LC-MS/MS, 1D SDS-PAGE | Lampetra morii | Novel proteins involved in blood coagulation suppression and host immune evasion during feeding were identified. | [114] |
Reproductive processes in seminal plasma | HPLC-ESI-MS/MS, 2D-DIGE | Oncorhynchus mykiss, Cyprinus carpio | Identified proteins regulating sperm motility, membrane stability, antioxidative defense, and inflammation responses. | [107,115] |
Growth and muscle development | DIGE, MALDI-TOF/TOF | Sparus aurata | Proteins such as parvalbumins and Wap65 were linked to growth, stress adaptation, and dietary influences. | [116,117] |
Gill proteome analysis | Data-independent acquisition | Gasterosteus aculeatus | Explored molecular differences in gill proteins among ecotypes, revealing adaptation to environmental and morphological variations. | [118] |
Lymphoid organ function | Shotgun proteomics | Oncorhynchus mykiss | Profiling of head kidney and spleen proteins provided insights into immune mechanisms and DNA repair processes. | [119] |
Confirmation of specific proteins | LC-MS/MS | Gadus morhua | Verified the presence of natterin-like proteins in skin, liver, and kidney, linked to immune responses. | [120] |
3.2. Disease Resistance and Immunity
3.3. Environmental Adaptation and Stress Response
Stressors | Technique Used | Species | Findings | References |
---|---|---|---|---|
Physical stress | ||||
Overcrowding | LC-MS/MS, 2-DE | Sparus aurata | Liver and immune proteins showed significant changes under overcrowding compared to optimized rearing conditions. | [136,137] |
2-DE | Salmo salar | Proteins in muscle and plasma revealed secondary and tertiary stress responses. | [138] | |
X-ray irradiation | LC-MS | Salmo salar | Persistent alterations in gill proteins observed in early-stage rainbow trout. | [139] |
Freezing conditions | 2-DE, MALDI-TOF/TOF MS | Cyprinus carpio | Sperm proteins supported antioxidative defense, membrane stability, and motility control. | [140,141] |
High temperature | LTQ-Orbitrap XL | Salmo salar | Proteomic changes in the liver indicated reduced energy expenditure to cope with oxidative stress. | [142] |
Low temperature | iTRAQ | Takifugu fasciatus | Enhanced oxidative stress response and mitochondrial enzyme activity were linked to cold tolerance. | [143] |
Hypersalinity | LC-MS | Unspecified | Differentially expressed proteins supported osmoregulation, digestion, and mineral regulation in response to salinity changes. | [144] |
High CO2 and temperature | 2-DE, Nanoflow LC-MS/MS | Hippoglossus hippoglossus | Energy metabolism proteins in gills and immune proteins in blood plasma were significantly affected. | [145] |
Chemical stress | ||||
Copper | 2D-DIGE, iTRAQ | Oncorhynchus mykiss, Cyprinus carpio, Carassius auratus gibelio | Oxidative stress markers, such as superoxide dismutase and cytochrome c, were identified in gills. | [146] |
Arsenic | 2D, MALDI-TOF/TOF MS | Labeo rohita | Identified biomarkers (Apo-A1, A2ML, Wap65) indicate arsenic-induced liver toxicity. | [147] |
Benzotriazole | 2-DE, TOF/TOF MS/MS | Gobiocypris rarus | Neurological and liver alterations differed between male and female fish. | [148,149] |
PAHs (Polycyclic Aromatics) | LC-MS/MS | Gadus morhua | An albumin-like protein in plasma was linked to PAH-induced stress. | [150] |
PCB (Polychlorinated Biphenyl) | MALDI-TOF MS, MS/MS | Gadus morhua | Proteins linked to neurotoxicity and stress pathways (e.g., Notch signaling) were identified. | [151] |
Bisphenol A | LC-MS/MS | Danio rerio | Proteomic changes in brain tissue suggested complex toxicity mechanisms involving metabolism and transport. | [152] |
Pesticides (Permethrin, Terbufos) | LC-MS/MS | Pimephales promelas | Enrichment of proteins associated with proteasome systems and glycolysis was observed. | [153] |
Pesticide (Dieldrin) | LC-MS/MS, iTRAQ | Danio rerio | Mitochondrial proteins showed links to diseases like Parkinson’s and Huntington’s. | [154] |
Herbicide (Ametryn) | SDS-PAGE | Danio rerio | Induced proteins were linked to glycolysis and lipid transport, while suppressed proteins were associated with oxygen transport. | [155] |
3.4. Reproductive Biology and Hatchery Management
4. Challenges and Limitations in the Use of Proteomics in Livestock and Aquaculture Production
4.1. Management and Maintenance of Proteomics Data
4.2. Lack of Comprehensive Phenomics Data
4.3. Sample Preparation and Variability
4.4. Species-Specific and Tissue-Specific Challenges
4.5. Cost and Accessibility
5. Future Directions
5.1. Multi-Omics Integration and Systems Biology Approaches
5.2. Single-Cell and Spatial Proteomics
5.3. Proteogenomics and Proteotranscriptomics
5.4. Artificial Intelligence in Proteomics
5.5. Standardized Protocols and Data Sharing
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Jitjumnong, J.; Taweechaipaisankul, A.; Lin, J.-C.; Wongchanla, S.; Chuwatthanakhajorn, S.; Lin, C.-J.; Khang, L.T.P.; Linh, N.V.; Sangsawad, P.; Dinh-Hung, N.; et al. An Overview of Advancements in Proteomic Approaches to Enhance Livestock Production and Aquaculture. Animals 2025, 15, 1946. https://doi.org/10.3390/ani15131946
Jitjumnong J, Taweechaipaisankul A, Lin J-C, Wongchanla S, Chuwatthanakhajorn S, Lin C-J, Khang LTP, Linh NV, Sangsawad P, Dinh-Hung N, et al. An Overview of Advancements in Proteomic Approaches to Enhance Livestock Production and Aquaculture. Animals. 2025; 15(13):1946. https://doi.org/10.3390/ani15131946
Chicago/Turabian StyleJitjumnong, Jakree, Anukul Taweechaipaisankul, Jou-Ching Lin, Supatirada Wongchanla, Schwann Chuwatthanakhajorn, Chih-Jen Lin, Luu Tang Phuc Khang, Nguyen Vu Linh, Papungkorn Sangsawad, Nguyen Dinh-Hung, and et al. 2025. "An Overview of Advancements in Proteomic Approaches to Enhance Livestock Production and Aquaculture" Animals 15, no. 13: 1946. https://doi.org/10.3390/ani15131946
APA StyleJitjumnong, J., Taweechaipaisankul, A., Lin, J.-C., Wongchanla, S., Chuwatthanakhajorn, S., Lin, C.-J., Khang, L. T. P., Linh, N. V., Sangsawad, P., Dinh-Hung, N., Tang, P.-C., & Moonmanee, T. (2025). An Overview of Advancements in Proteomic Approaches to Enhance Livestock Production and Aquaculture. Animals, 15(13), 1946. https://doi.org/10.3390/ani15131946