Unveiling the Role of Proteomics in Revolutionizing Aquafeed Development
Proteomics is the study of the proteome, which comprises all the proteins expressed by cells in an organism at any given point in time. Despite its relative infancy, proteomics is becoming an increasingly valuable tool in aquaculture by enabling a deeper understanding of fish biology. This is essential in improving fish health, nutrition, as well as overall welfare, in the industry’s bid to be a more sustainable production system in light of increasing global food demands. These demands are compounded by the growing need for high quality, sustainable feed ingredients in aquaculture, particularly as we move away from unsustainable sources like fishmeal. But assessing the impact of novel feed ingredients on fish and their environments requires a more holistic approach for a better understanding of fish biology. While proteomics has a multitude of applications, this article explores how proteomics offers a novel approach to assessing the effects of emerging novel feed ingredients.
Aquafeed is a rapidly growing sector, where more than 60% of an aquaculture farm’s overheads are attributed to feed
i. The Aquafeed Challenge
The growing global demand for high quality protein, and the significant technological strides witnessed in aquaculture, has made this the fastest growing food industry in the world. The global consumption of fish has increased by 120% since the early 90’s, with more than 50% of the fish we currently consume sourced from aquaculture production. These figures are only set to rise by 15% by 2030, particularly as we witness changes in dietary trends from conventional meat production towards more healthier, sustainable protein sources. With growing consumer awareness and demand for ethically produced fish, it stands to reason that the purported sustainability of aquaculture comes into question when we address aspects of the supply chain, such as feed production.
How can we sustainably feed farmed fish that is intended to feed the growing global demand? Traditionally, fishmeal has been primarily used as a protein source in commercial feeds, but, notwithstanding the resource intensive nature of fishmeal production, many forage fish populations have become increasingly overfished, leading to a plethora of environmental knock-on effects. I will not delve further into this, since the challenges associated with fishmeal, and soy meal, are widely documented. However, this has led the industry to address how they can sustainably identify and utilize novel feed ingredients, replacing conventional ones, that provide improved nutrition and efficiency, to produce high-quality fish for consumption, while ensuring the health and welfare of the animals themselves. To further compound these challenges, aquaculture producers are inherently mindful of high feed costs, with feed accounting for nearly 60% of a commercial farm’s overheads. As such, aquafeed producers are tasked with a mountainous task: utilizing ethical, low-impact nutritious feed ingredient alternatives that support high FCRs, improved animal health and welfare, while remaining cost-effective for their clients.
ii. What is Proteomics?
Proteomics is like a vast library that documents and details every protein produced in an organism, providing comprehensive insight into the functional machinery of life. Being the gene complement, proteins are the workhorses of cells - the biomolecules that interact with one another to execute a meticulous array of cellular activities, such as metabolic processes, immune and stress responses, as well as reproduction. All omics platforms are essential fields of study in understanding biological systems, but proteomics offers several advantages over its counterparts:
1. While the genome may be considered the blueprint, the final architecture that is the proteome, is highly dynamic and dependent on various factors, such as protein-protein interactions and post-translational modifications. Unlike genomics and transcriptomics, proteomics can detect these modifications, providing functional insight into the state of proteins within a cell. For example, depending on the conditions (i.e. high temperatures), any combination of post-translational modifications can “tweak” the structure of certain proteins, which in turn “tweak” how the proteins function with other proteins in complex biological networks, to carry out a particular physiological response (i.e. response of an organism to high temperatures).
2. Proteomics employs incredibly sensitive equipment to identify thousands (currently around 3000) of proteins in biological samples. And due to the complex nature of proteins, proteomics analyses provide detailed insight into the structure, function and dynamic interplay of proteins within complex biological systems.
3. Since proteins are oftentimes the direct target for drug/vaccine treatment, while also being more closely linked to the physical traits of diseases, proteomics allows for the identification of these targets, as well as mapping the mechanisms of disease within an organism. Conversely, genomics is predominantly diagnostic in nature - identifying disease agents, and/or potential genetic predispositions.
4. Proteomics offers real-time insight into biological responses to changing environmental conditions, disease progression, nutrition, and disease treatments. As such, proteins serve as excellent molecules for biomarker discovery. This has led to proteomics becoming an increasingly popular tool for drug target discovery of cancer, where a simple Google Scholar search for research this year alone yielded over 9000 research papers detailing the use of proteomics in cancer biomarker research.
So, why not shift the potential proteomics holds in human health research and drug development to similar applications in aquaculture, and indeed other animal production sectors?
Proteins carry out a myriad of functions in complex pathways such as nutrient absorption and utilization, immune and stress responses, as well as tissue regeneration and growth.
iii. Proteomics in Feed Ingredient Assessment
As the demand for sustainable alternative protein sources in aquafeed grows, the use of proteomics is increasingly enabling researchers with deeper biological insights to make more informed decisions in their research and development endeavors. In this section, we’ll explore how proteomics is transforming feed ingredient assessment in three key areas: evaluating the quality and digestibility of novel ingredients, identifying beneficial bioactive peptides, and assessing anti-nutritional factors in plant-based proteins. These applications of proteomics are not just advancing our scientific knowledge, but are also paving the way for more sustainable, nutritious, and cost-effective aquafeeds that can support a rapidly growing industry.
Assessing protein quality and digestibility of novel ingredients
The depth of biological data attainable from proteomics allows for the identification and quantification of proteins in emerging feed ingredients, the evaluation of protein-protein interactions that may affect digestibility, as well as comparing digestibility patterns between conventional and novel ingredients. For example, an increasing number of studies are utilizing proteomics for assessing the quality and digestibility of insect meals, algae-based proteins, and single-cell proteins, as fish meal replacements. This study utilized an integrated proteomics and metabolomics approach to assess varying insect meal inclusion levels in aquafeed fed to juvenile rainbow trout. The outcomes detailed in the article paint a comprehensive picture of the biological and dietary modulation of trout metabolism, buttressing the importance of undertaking a multi-layered approach to assessing emerging ingredient alternatives in fish feed. In another study, proteomics was utilized for assessing the impact of essential amino acid supplementation in a plant-based diet in seabream - an approach for improving plant protein quality for complete substitution of fish meal in aquafeeds. Again, proteomics offers the level of biological insight required for ensuring optimal feed formulations with novel feed ingredients.
Identifying and characterizing bioactive peptides in feed ingredients
Proteomics analysis offers not only quantitative assessments, but the use of a robust bioinformatics pipeline unlocks a plethora of functional and physiological insights that inform effective farming and feeding practices in animal production. Proteomics helps in identifying peptides in novel feed ingredients with potential health benefits for fish, as well as allowing researchers to track the release of these bioactive peptides during digestion, thereby characterizing their antimicrobial/antioxidant/immunoregulatory properties for functional feed development. For example, this study utilized proteomics to comprehensively characterize salmon protein hydrolysate and validate its safe use in feed formulations for farmed salmon. With the use of proteomics, researchers were able to map the nutritional benefits of salmon hydrolysate, while also screening for prion proteins that can cause degenerative diseases if reused in the same species. Data showed salmon hydrolysate to be a promising and safe novel feed ingredient, with a highly nutritious amino acid profile.
Evaluating anti-nutritional factors
As the aquafeed sector looks to more sustainable alternative protein ingredients like plant protein, it is becoming increasingly important to evaluate them and their anti-nutritional factors. This is particularly important not only for ensuring feed palatability, digestibility, and nutrient availability, but for understanding the economic implications (i.e. certain anti-nutritional factors can in fact reduce feed efficiency, thereby increasing production costs), as well as optimal processing methods during feed production. Additionally, understanding the species-specific effects of anti-nutritional factors in plant-based protein on health and growth performance, ultimately informs optimal feed feed formulations, while abiding to regulatory compliance. In a study assessing the gut proteome of gilthead seabream fed with a fishmeal-based diet, against plant protein-based diets with or without alternative marine ingredients inclusion, researchers found that the plant-based only diet led to sub-optimal gut performance through a downregulation of proteins involved in inflammatory responses, epithelial permeability, as well as nutritional absorption. Conversely, the data from the combined diet treatment suggested a mitigating effect of the marine ingredients inclusion to anti-nutritional factors observed in fish fed the plant-based only diet. Indeed, this study shows how understanding the levels and types of anti-nutritional factors in plant proteins allows for more precise and effective feed formulations, where potentially combining ingredients can offset some of the negative effects.
iv. The Future of Aquafeed Development
As the aquaculture industry continues to grow, public pressure and tightening regulations on sustainability and improved animal welfare will be the defining factors on the success of the industry. Recent perspectives from industry experts at the North Atlantic Seafood Forum, for example, believe that there is an urgent need for unlocking and driving investment into biotech solutions for solving and/or mitigating health and welfare challenges in large-scale fish farming. This was further buttressed in the many talks alluding to the major gaps in our knowledge on fish biology, particularly in the context of optimal farming setups and nutrition. Enough research suggests that one avenue for optimizing fish health and welfare, and improving the sustainability of the industry, is in effective feed formulations and optimal nutrition. And over the last 5 - 10 years the aquafeed sector has witnessed substantial growth and investment in research and development, particularly as it shifts its gaze to more sustainable ingredient sources. Through a holistic approach to research with emerging technologies, like proteomics, that offer an immense depth and wealth of biological data, aquafeed development could be transformative in a number of ways, not least of all:
Precision nutrition - enhanced tailoring of feeds to species, life stages, and even genetic strains.
Holistic insight - the integration of multi-omics (i.e. proteomics, metabolomics, genomics etc) approaches that will offer unparalleled biological knowledge on fish nutrition and physiology.
Precision in biomarker discovery - more accurate identification and characterization of biomarkers of fish health, stress and nutritional status, that enable the development of biosensors and rapid diagnostic tools.
Predictive modeling - the integration of proteomics data with machine learning models will enable the prediction of outcomes of different feed formulations and novel feed ingredients, thus fast-tracking research and development.
Plant-based protein and algae are some of the novel alternative ingredient sources being explored for fishmeal replacement.
v. Conclusion
Proteomics has emerged as a powerful tool - offering unprecedented insights into fish nutrition at the molecular level. By allowing us to delve deep into the complexities of protein interactions, metabolism, and bioavailability, proteomics is transforming our approach to aquafeed development. From assessing novel ingredients and identifying bioactive peptides, to evaluating anti-nutritional factors and comparing protein profiles, technologies like this are paving the way for more efficient, sustainable, and safe feed formulations. As we continue to harness the power of proteomics, we can expect to see feeds that not only optimize fish growth and health, but also contribute to the overall sustainability of the aquaculture industry.
The integration of proteomics with other advanced technologies promises a future where aquafeeds are precisely tailored to the needs of specific fish species, life stages, and farming conditions. This revolution in feed development will play a crucial role in meeting the growing global demand for seafood while minimizing environmental impacts. As we move forward, the continued application and advancement of proteomic techniques in aquafeed research will undoubtedly be a key factor in shaping the future of aquaculture. By embracing this technology, we are not just feeding fish; we are feeding innovation, sustainability, and the future of food security.
Sources
The State of World Fisheries and Aquaculture 2022
Carrera, M. et al. Proteomic Strategies to Evaluate the Impact of Farming Conditions on Food Quality and Safety in Aquaculture Products. 2020. Foods, 9:1050.
