Nutrigenomics in Aquaculture: Optimizing Health and Nutrition Through Gene Expression

Over the last decade, the aquaculture industry has evolved from an empirical activity into a precision science, with nutrigenomics serving as a fundamental pillar of this transformation. Given the rising global population and the increasing demand for aquatic proteins, developing efficient and sustainable diets has become a strategic imperative. Nutrigenomics seeks not merely to feed a species, but to ‘interact’ with its genes to maximize health, growth, and resilience.

Traditional approaches to feed formulation often overlook the complex interactions between diet, physiology, and the environment (Saluja et al., 2026); in response, nutrigenomics has emerged as a disruptive solution. Today, this discipline has moved beyond the ‘proof of concept’ phase to establish itself as a practical toolkit for designing species-specific functional feeds tailored to biological stages. In this article, we will explore the significance, tools, and challenges of nutrigenomics, integrating key concepts of epigenetics, biotechnology, and functional nutrition.

Key Takeaways: The Future of Aquaculture Nutrigenomics

• From Observation to Precision: The industry has transitioned from ‘trial and error’ methods to a precision science, directly ‘engaging’ with fish and shrimp genomes to optimize performance.

• Nutritional Programming (The ‘Memory Effect’): Nutritional stimuli during larval stages can metabolicly ‘prime’ organisms, enabling carnivorous species to efficiently utilize plant-based diets in adulthood.

• Gut Health and Functional Diets: Transcriptomics allows for the molecular detection of enteritis and metabolic stress before clinical signs appear, facilitating the design of feeds that serve as immunological ‘shields.’

• The Power of Epigenetics: Broodstock nutrition (maternal nutrition) imprints molecular marks on offspring that enhance growth and resilience—a vital advancement for hatchery profitability.

• Convergence with Artificial Intelligence: The near future integrates multi-omic data with AI predictive models to create dynamic feed formulas that adjust in real-time to the animal’s physiological state and environment.

• Economic Efficiency: Precision nutrition transcends science into profitability; reducing culture cycles and improving Feed Conversion Ratios (FCR) transforms the cost structure of any aquaculture operation.

What is Nutrigenomics? Definition and Fundamental Concepts

To grasp the impact of this discipline, it is essential to define the precise meaning of nutrigenomics. In simple terms, it is the study of how nutrients and dietary components influence an organism’s gene expression.

Definition and Technical Scope

Nutrigenomics applies advanced genomic tools—such as transcriptomics—to analyze the nutritional impact on a species’ transcriptome, proteome, and metabolome. In the aquaculture sector, this science investigates how ingredients interact with the genomes of fish and crustaceans to modulate their molecular response. Unlike classical nutrition, this discipline seeks to optimize health, growth, and sustainability through genetic modulation. Several authors support its strategic relevance:

• Hakim et al. (2018): Highlight that nutrigenomics explains why different species process food differently, such as variations in carbohydrate digestion between carnivorous and herbivorous fish.
• Mohanty et al. (2020): Defines its practical objective as understanding individual responses to food to design personalized diets based on genetic makeup.
• Zehra et al. (2025): Notes that it enables the development of species- or strain-specific formulas, satisfying unique metabolic needs through “precision diets.”
• Muhamad et al. (2025): emphasize that this science bridges nutrition and molecular biology to explore how dietary inputs determine phenotypic outcomes in aquatic species.

In practice, this allows us to understand why certain ingredients enhance development, while others may trigger inflammation or metabolic stress processes.

Nutrigenetics vs. Nutrigenomics: Key Differences

While these terms are often confused, they represent two complementary dimensions of molecular nutrition:

1. Nutrigenetics (Individual Variability): Focuses on how genetic variations (such as polymorphisms or SNPs) influence the response to diet. For example, it explains why certain Atlantic salmon lineages utilize Omega-3 fatty acids more efficiently than others.
2. Nutrigenomics (Response to Stimuli): Studies the inverse effect; that is, how dietary components alter gene expression.

While nutrigenetics helps select individuals with superior metabolic capabilities, nutrigenomics optimizes feed so that these individuals can reach their maximum genetic potential.

Pro-Tip: The synergy between both disciplines allows for a reduction in the culture cycle by aligning the specimen’s genetic profile with a high-precision nutritional program.

Omic Tools: The Arsenal of Modern Aquaculture

The application of nutrigenomic tools is the central axis for addressing critical challenges in larviculture and aquaculture production. According to Gargotra and Aakash (2026), the integration of “omic” technologies provides unprecedented precision regarding nutrient-gene interactions, metabolic pathways, and microbiome dynamics. Furthermore, Saluja et al. (2026) define this approach as an integrative strategy that enables the development of species-specific diets to maximize biological performance.

The “Omics” Discipline Ecosystem

Based on research by Chuphal and Singha (2026), Iyyapparaja et al. (2022), and Mohanty et al. (2020), the key contributions of each discipline are presented below:

Genome Editing Technologies: The Potential of CRISPR/Cas9

Genome editing via CRISPR/Cas9 is redefining aquaculture biotechnology. While nutrigenomics adjusts the “software” (gene expression), CRISPR allows for editing the “hardware” (the genetic code) to enhance desirable traits. According to Khan (2026), integrating CRISPR with nutrition will enable disruptive applications:

• Carnivorous fish with herbivorous enzymes: Enabling carnivorous species to digest plant-based ingredients, eliminating dependence on fishmeal.
• Shielded microbiomes: Designing pathogen-resistant gut bacteria to protect fish naturally.
• Next-Generation Editing: Tools like Prime Editing and Base Editing offer surgical precision to correct individual letters of the genetic code without damaging the DNA strand.

Legal Disclaimer: The use of genetically edited organisms is subject to strict international regulations. Consumer acceptance currently remains the greatest challenge for commercial implementation.

Key Advancements and Future Applications

Technological convergence is accelerating industry results (according to Ibrahim et al., 2025 and Zhang et al., 2025):

• Input Substitution: Development of strains capable of endogenous synthesis of Omega-3 fatty acids (EPA and DHA), reducing fish oil usage.
• Reference Genomes: Access to high-quality genomes (salmon, trout, tilapia) facilitates the discovery of specific nutrigenomic markers.
• Predictive Bioinformatics: Advanced workflows allow for models that predict the relationship between diet, immunity, and health before the culture cycle begins.

The Molecular Biology of Nutrition: Epigenetics and Gene Expression

Nutrigenomics in fish and crustaceans relies heavily on epigenetics—the study of heritable changes in gene function that do not alter the original DNA sequence, but rather its execution.

DNA Methylation and Growth Regulation

One of the most extensively studied mechanisms in teleost fish is DNA methylation. Biochemically, the addition of a methyl group to cytosine residues within $CpG$ dinucleotides is typically associated with the silencing of specific genes. This process can be represented by the following enzymatic interaction:

$ADN + SAM \xrightarrow{DNMT} ADN\text{-}CH_{3} + SAH$

In modern aquaculture, nutritional factors such as methionine or choline levels can alter these methylation patterns. This directly impacts genes responsible for growth regulation and resilience to environmental stress.

The Role of mRNA and Transcriptomics

Transcriptomics stands as the master tool of nutrigenomics. By quantifying messenger RNA ($mRNA$) levels, researchers determine which genes are activated or deactivated in response to a diet. For instance, if a species receives excessive levels of plant protein, transcriptomics can reveal the up-regulation of pro-inflammatory genes in the gut, alerting to the risk of enteritis before physical symptoms become visible.

Current technologies have enabled significant milestones, according to experts:

• Geetha and Sarumathiy (2024): Report that Next-Generation Sequencing ($RNA\text{-}seq$), combined with bioinformatic tools such as DESeq2 and EdgeR, allows for the discovery of genes that are differentially expressed in response to minimal nutritional changes.
• Khan (2026): Classifies DNA microarrays and $RNA\text{-}seq$ as essential “omic” technologies for analyzing $mRNA$ transcription outputs and understanding nutrient influence at the molecular level.

Genomic Diagnostic Tools

According to scientific evidence, these tools are applied in the aquaculture field as follows:

• DNA Microarrays: Offer a comprehensive view of the genomic response by analyzing thousands of genes simultaneously. Although powerful, Khan (2026) notes that their use still faces limitations due to the need for species-specific genetic markers.
• RNA-seq: This advanced technology allows for the observation of how components like Omega-3 fatty acids can attenuate cytokine excess during viral infections by up-regulating interferon genes and Natural Killer ($NK$) cells to combat pathogens.

Applications of Nutrigenomics: Transforming Aquaculture Production

The transition from a “trial and error” model toward precision nutrition represents the most disruptive advancement of the decade. According to Khan (2026), current applications allow for production optimization across four strategic axes:

Metabolic Optimization Strategies

• Species Differentiation: Nutrigenomics explains why carnivorous fish face difficulties assimilating carbohydrates due to insulin dysregulation. In contrast, it identifies how herbivorous fish activate specific enzymes to process these inputs, facilitating more cost-effective diets.
• Protein and Lipid Efficiency: By reducing protein and increasing lipids through “genomically guided” methods, protein synthesis is enhanced while nitrogen waste is minimized. This protects fillet quality and reduces environmental pollution without causing excessive visceral fat accumulation.
• Immunological Precision Diets: Specific nutrients act as genetic “switches.” For instance, n-3 PUFAs (Omega-3) reduce viral load and inflammation, while selenium hyper-stimulates natural antiviral defenses.
• Designer Feeds: The ultimate goal is to maximize the Feed Conversion Ratio (FCR) and accelerate compensatory growth, thereby shortening the culture cycle and reducing environmental impact.

Overcoming Hatchery Challenges and Environmental Stress

Early mortality and cannibalism are often symptoms of nutritional imbalances invisible to the human eye.

• Iyyapparaja et al. (2022) emphasize that omic tools are vital for understanding how nutrition affects cellular response during critical developmental stages.
• Hays et al. (2023) demonstrated that precise supplementation (such as 1.2% taurine in turbot) positively stimulates growth genes and enriches essential metabolic pathways.
• Mitra et al. (2023) highlight a vital application in the face of the climate crisis: dietary modification to mitigate physiological stress from temperature changes, strengthening natural immunity through gene expression.

Summary of Advancements by Biological Traits

Early Nutritional Programming: The Power of the Beginning

A disruptive concept in the industry is Early Nutritional Programming. This phenomenon demonstrates that stimuli received during larval stages can “program” a fish’s metabolism for the rest of its life, optimizing its performance through adulthood.

Training Metabolism from Birth

Metabolic programming consists of using specific larval diets to “precondition” enzymatic pathways. According to Hou and Fuiman (2020), this developmental plasticity coincides with periods of high mortality, allowing nutrition to be employed as a strategic tool for survival and sustainability.

Kumar et al. (2026) summarize the competitive advantages of this approach:

• Permanent Effects: Interventions during embryonic, larval, and juvenile phases induce physiological and neurological changes that persist for a lifetime.
• Maternal Inheritance: Nutrients transferred from the mother via the yolk sac dictate initial viability. Substituting fish oils with vegetable oils in the maternal diet can “teach” offspring to better tolerate and process these alternative sources in the future.
• The Power of First Feeding: The first external feed shapes digestive capacity. A brief early exposure to carbohydrates leads to a prolonged increase in the activity of enzymes such as amylase, enabling carnivorous species to efficiently assimilate plant-based diets in adulthood.

The Epigenetic Engine and the TOR Pathway

The mechanism behind this metabolic memory is epigenetics. Alterations such as DNA methylation and histone modification adapt the fish’s phenotype to its environment without altering its genetic code.

In larviculture, the clearest example is the use of specific amino acids to activate the TOR (Target of Rapamycin) signaling pathway, which is responsible for protein synthesis. Hakim et al. (2018) emphasize that these effects are so profound that they can even be transmitted to subsequent generations, impacting overall growth and immune response.

Advancements in Larval Development

Despite knowledge gaps regarding neurological development, technologies such as $RNA\text{-}seq$ are enabling the design of specific micro-diets.

• Iyyapparaja et al. (2022): Note that genetic precision will allow for the creation of tailored diets to maximize hatchery survival.
• Martínez-Burguete et al. (2021): Identified for the first time the transcriptomic profiles of the tropical gar (Atractosteus tropicus), establishing candidate markers to monitor digestive system development.

Impact of Nutritional Components on Development

Immunity, Functional Feeds, and Gut Health

Immune function in aquatic organisms is intrinsically linked to their nutrition. Nutrigenomics has uncovered how functional feeds modulate biological responses at a molecular level, transforming disease prevention into a precision science.

Modulation of the Immune Response

According to Martin and Król (2017), the strategic use of additives—such as prebiotics (beta-glucans and oligosaccharides), phytochemicals, and specific marine oils—enhances natural resistance. Khan (2026) reinforces this concept, reporting that nutrigenomics enables the exact identification of how these components regulate gene expression within both innate and adaptive immune pathways.

The Challenge of Plant-Based Proteins and Oils

The transition toward plant-derived ingredients (soy, pea) due to fishmeal scarcity has presented critical challenges that transcriptomics helps mitigate:

• Intestinal Inflammation: Certain anti-nutritional factors in plants trigger adverse responses. Transcriptomic studies cited by Martin and Król (2017) reveal that soy rapidly activates inflammatory mediator genes, which can lead to intestinal epithelial barrier dysfunction, thereby facilitating pathogen entry.
• Fasting Management: Nutrient deprivation reduces the expression of key immune system components to conserve energy. However, fasting fish exhibit a disproportionate “acute-phase” response to infections in an attempt to compensate for diminished prior defenses. Furthermore, fasting significantly weakens the mucosal immune system in the skin and gills.

Strategic Comparison: Traditional Nutrition vs. Nutrigenomic Approach

Sustainability: Plant-Based Proteins and Alternative Oils

The transition toward fishmeal-free diets represents the greatest challenge in modern aquaculture. In this scenario, nutrigenomics is positioned as the definitive tool for understanding why carnivorous species develop pathologies such as enteritis when ingesting plant proteins, enabling the selection of ingredients that do not trigger inflammatory pathways.

Challenges of the Nutritional Transition

The use of vegetable oils and plant proteins is an ecological and economic necessity. However, these inputs contain anti-nutritional factors (ANFs) that can compromise the integrity of the intestinal epithelium. Nutrigenomics allows for the mapping of these adverse responses to formulate diets that mitigate cellular damage. According to the most recent research:

• Gargotra and Aakash (2026): Strategies based on “omic” disciplines facilitate the adoption of sustainable alternatives, such as insect meal and algal biomass, fostering the efficient use of non-marine resources.
• Zamzami et al. (2025): By decoding metabolic pathways, it is possible to maintain production performance in shrimp using plant or microbial protein sources. This reduces dependence on finite inputs and supports the development of low-impact aquaculture systems aligned with global SDGs (Sustainable Development Goals).

Toward an “Herbivorous Metabolism” in Carnivores

One of the most disruptive advancements is the use of nutritional programming to “teach” species such as salmon to process carbohydrates efficiently. Although their genome is not naturally designed for this purpose, manipulating gene expression from early stages allows for a forced metabolic adaptation, optimizing the use of terrestrial inputs in traditionally carnivorous species.

Knowledge Gaps and Future Challenges

Despite the disruptive potential of fish nutrigenomics, the industry faces critical hurdles that must be overcome to achieve widespread and standardized implementation:

• Causality vs. Correlation: It is fundamental to move beyond observing which genes are activated to understand the biological “why,” determining if such changes are the direct drivers of observed growth.
• Lack of Full-Cycle Studies: Most current research is short-term. Longitudinal studies are required to monitor organisms from the larval stage through to harvest.
• Standardization of Protocols: Variability in results between laboratories highlights the need for unified methods for epigenetic assays in aquatic species.
• Antinutrient Synergy: A knowledge gap persists regarding how multiple anti-nutritional factors (ANFs) interact at the molecular level when combined in a single diet.

The Future: Artificial Intelligence and Precision Nutrition

The evolution of the discipline points toward massive data integration. According to Uvarajan (2024), combining genomic, proteomic, and metabolomic levels will feed Artificial Intelligence (AI) predictive models. This will allow for the formulation of diets that dynamically adapt to the physiological state of each species, maximizing profitability and minimizing nutrient waste. Strategic directions for 2025–2026 include:

• Precision Nutrition Frameworks: Integration of genotype and environment to design “tailored feeds” (Ibrahim et al., 2025; Zhang et al., 2025).
• Nutritional Immunomodulation: Utilizing nutrigenomics to optimize immunostimulants, seeking total resilience and the elimination of antibiotics (Kari, 2025).
• Multi-omic Integration: Identifying durable nutritional markers through the study of non-coding RNA (ncRNA).

Pending Challenges and Global Vision

As noted by Zehra et al. (2025) and Gargotra & Aakash (2026), the future lies in personalized feeding strategies that ensure global food security. However, to get there, we must address three pillars:

1. Multigenerational Studies: Confirming whether the epigenetic benefits of broodstock diets are stably inherited.
2. Fillet Quality: Linking gene expression to the final texture, color, and nutritional profile of the commercial product.
3. Regulatory and Social Framework: There is an urgent need to educate policymakers and consumers on the safety and benefits of these biotechnologies.

Conclusion: Toward Precision Aquaculture

Nutrigenomics in aquaculture has evolved from an academic trend into the master key for sustainable “blue production.” By integrating nutritional science with molecular genetics, it is now possible to develop diets that not only maximize growth but also guarantee animal welfare and drastically reduce the industry’s environmental footprint.

This discipline is laying the groundwork for a new generation of “smart feeds” driven by omic data. As noted by Zamzami et al. (2025), these formulas synergistically integrate antioxidant regulation, immunological conditioning, and precision engineering of the gut microbiome.

Ultimately, nutrigenomics has displaced the outdated “trial and error” model in favor of an approach based on exact biological mechanisms. Although challenges remain regarding long-term effects and species-specificity, the sector’s future lies in our ability to decipher the dialogue between nutrients and the genome. As we bridge current technical gaps, aquaculture will undoubtedly position itself as the most efficient, sustainable, and technologically advanced animal protein production sector on the planet.

Frequently Asked Questions (FAQ) about Aquaculture Nutrigenomics

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Milthon Lujan

Editor at the digital magazine AquaHoy. He holds a degree in Aquaculture Biology from the National University of Santa (UNS) and a Master’s degree in Science and Innovation Management from the Polytechnic University of Valencia, with postgraduate diplomas in Business Innovation and Innovation Management. He possesses extensive experience in the aquaculture and fisheries sector, having led the Fisheries Innovation Unit of the National Program for Innovation in Fisheries and Aquaculture (PNIPA). He has served as a senior consultant in technology watch, an innovation project formulator and advisor, and a lecturer at UNS. He is a member of the Peruvian College of Biologists and was recognized by the World Aquaculture Society (WAS) in 2016 for his contribution to aquaculture.