Alternatives to fishmeal are becoming increasingly important as the aquaculture industry faces rising long-term prices and supply constraints. To adapt, the industry should diversify its raw materials with alternative proteins that deliver equivalent nutritional value. Among these alternatives, single-cell proteins stand out as strong candidates that could partially or entirely replace fishmeal and reduce supply uncertainties.
Product Manager – Functional Health Ingredients
Unibio A/S
Anyone familiar with aquaculture nutrition knows there has been a longstanding global concern about the sustainability of fishmeal as an ingredient, both in environmental and economic terms. Those who have been in the field for the past 20-30 years know that this concern has been partially addressed by plant-based ingredients, an approach that is attractive in terms of cost but not ideal for fish gut health.1 If we narrow the timeframe further, anyone who has been in the sector over the past 15 years will know that there is now a growing number of promising alternatives aimed at reducing the pressure on the planet’s resources, ranging from animal-sourced ingredients (such as poultry by-products and insect meals) to microalgae and fermented proteins derived from single-cell biomass.2
A quick search on fermentation technologies and other single-cell culture methods for biomass production suggests that several hundred microorganism strains have been cultured for food or feed in recent years. If we limit it to cases with commercial potential, the number of strains studied ranges between 150 and 300. If we further narrow it to those included in significant amounts in aquaculture feed, the count falls to between 15 and 30 strains, which is still a very significant number.3
TYPES OF BIOMASSES
Yeast
Among the numerous microorganisms studied, yeast is one of the most extensively researched and widely commercialized sources of single-cell protein, with many competitive products currently available in food and feed supply chains. These products often show high protein content, but beyond protein, one of the most interesting features of yeast is the presence of cell wall components such as beta-glucans. Beta-glucans are known enhancers of the innate immune response and can interact with immune receptors to promote a defensive reaction. This immunostimulatory effect is particularly valuable in aquaculture since fish are not naturally exposed to high levels of beta-glucans, which makes these compounds effective functional ingredients.4,5
Microalgae
Microalgae are gaining recognition as a promising and scientifically validated protein source for aquaculture. These tiny organisms offer impressive nutritional value. For example, Chlorella vulgaris and Spirulina platensis can contain up to 70% protein by dry weight and provide an amino acid profile that fulfills the needs of several fish species. Their wide biological diversity allows producers to develop tailored feed formulations that address the dietary needs of specific aquaculture species. One notable genus of green microalgae, Nannochloropsis, is naturally high in eicosapentaenoic acid (EPA), a long-chain omega-3 polyunsaturated fatty acid essential to fish health and development.6
In addition to their nutritional benefits, many microalgae species can grow in saline or wastewater environments. This makes them a practical choice for integrated production systems that aim to reduce environmental impact.7 As research progresses, advances in strain selection and metabolic engineering will further refine the use of microalgae to meet species-specific nutritional needs. Considering all of the above, microalgae is a strong candidate for the next generation of sustainable protein sources for aquafeed.
Microbial (bacterial)
Another type of biomass with a promising outlook is microbial biomass. As some of the simplest organisms on the phylogenetic scale, bacteria can devote more energy to pure growth and achieve some of the highest biomass production ratios known in nature. This relative simplicity, combined with millions of years of evolution, has enabled the development of numerous production methods, allowing bacteria to thrive and adapt to diverse ecological and industrial environments. These cultivation advances have also facilitated the development of bacteria-based production systems using diverse carbon feedstocks.
Sugar-based bacteria, such as Corynebacterium glutamicum, convert carbohydrates into protein-rich biomass, allowing agricultural by-products or waste sugars to be used as feedstock. Methanol-based bacteria, such as Methylobacterium species, utilize methanol, a simple one-carbon molecule often derived from industrial processes. Similarly, methanotroph bacteria consume methane, a potent greenhouse gas, and convert it into nutritionally valuable biomass that has shown good results for aquaculture feeds. These methanotroph bacteria naturally thrive at the bottom of lakes, where they play a key role in methane consumption as part of their life cycle and serve as an important protein source for fish and other aquatic organisms. Today, this natural process is being replicated at industrial scale to produce protein biomass.8,9
with Uniprotein® in rainbow trout feed
(Ruiz et al.,2023)
A recent study by Ruiz et al. (2023) showed that Uniprotein®, a protein-rich biomass produced by methane-fed microbes, can replace up to 100% of fishmeal in a rainbow trout feed formulation (15% total feed inclusion). No statistical differences were found in growth performance. A quadratic regression analysis further indicated that replacing approximately 42% of the fishmeal would be optimal for this formulation in rainbow trout, corresponding to about 6% Uniprotein® inclusion in the feed.10 In commercial settings, however, nutritionists at large feed companies are implementing 8% inclusion as a practical sweet spot (Figure 1).
CHOOSING THE RIGHT INGREDIENT
All the mentioned single-cell organisms, among others, demonstrate how flexible and useful they are as ingredients in aquaculture feed. However, treating these ingredients as if they belong to the same category would be a mistake, as there are important differences among them.
When approached from a ‘beyond protein’ perspective, the pathogen-associated molecular patterns (PAMPs) found in yeast and bacteria become particularly appealing. For instance, yeast contains beta-glucans in its cell wall, while bacteria contain lipopolysaccharides (LPS) in their membranes. As the name suggests, PAMPs are molecules associated with pathogens that can interact with components of the immune system to activate the innate immune response. When PAMPs are used within studied dosage ranges, they can act as natural immunological enhancers in fish.11
As for microalgae, one of their strongest advantages is their ability to provide a balanced fatty acid profile for fish, since there are few alternatives aside from fishmeal and fish oil that can do this. It is also worth mentioning that there is a vast variety of microalgae species with different nutritional compositions, something that could be applied to yeast and bacteria through strain selection and cultivation optimization. However, outside niche markets such as aquarium fish, the use of microalgae products is still quite limited due to price.
Another interesting point is that many of these ingredients tend to lower the omega-3 content in fish fillets. However, freshwater fish have a limited capacity to produce long-chain omega-3 fatty acids themselves, so feeding them well-studied, balanced diets can help compensate for this reduction. For example, a study by Ruiz et al. (2023) found that replacing 100% fishmeal with Uniprotein® (15% inclusion) did not disrupt the long-chain omega-3 polyunsaturated fatty acid profile of rainbow trout fillet. Despite complete fishmeal replacement, no significant differences were observed in fillet levels of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), or total long-chain omega-3 polyunsaturated fatty acids (Σ n-3 PUFA). This demonstrates that well-formulated diets can maintain essential fatty acid profiles in freshwater fish (Figure 2).
(Data from Ruiz et al., 2023)
SCALABILITY & SUSTAINABILITY
Going back to the topic of pricing, this brings us to one of the key advantages of methanotroph bacteria. Methane is abundant in natural gas reserves, and its price tends to fluctuate less than other raw materials. As a result, the cost of protein derived from methanotroph bacteria can remain relatively steady. This decouples it from the market volatility typically seen in agricultural and marine products. This pricing predictability is something that feed manufacturers and farmers undoubtedly will appreciate.
The relative stability in production costs gives methanotroph bacteria a competitive edge, but their true potential lies in scalability and environmental benefits. These bacteria convert methane into valuable protein, turning a climate challenge into a resource. This protein is high-quality, with an amino acid profile similar to fishmeal, and does not require as much arable land or freshwater as many plant-based alternatives. Additionally, industrial-scale fermentation facilities can operate continuously to ensure consistent and reliable protein production. This consistency is critical for large-scale aquaculture operations and feed manufacturing that aim to achieve the goal of sustainable feeds. Without scalability, not even the most promising protein sources can meet the growing demands of the industry.
Photos: Courtesy of Unibio
BREAKING DEPENDENCY ON FISHMEAL
According to a 2025 market forecast by Rabobank, the global fishmeal market is heading toward a shortage much sooner than previously expected12. The demand for fishmeal is becoming increasingly inelastic, and supplies are struggling to keep up with rising needs year after year. This tightening supply is leading to sharp price volatility, which poses challenges for the aquaculture industry that has long relied on fishmeal as a key feed ingredient. Fish do not actually need fishmeal itself; rather, they require the specific nutrients that fishmeal naturally provides. Fishmeal has traditionally been a staple ingredient in aquaculture feeds, as it contains a well-balanced mix of essential nutrients.
A high-quality nutritional profile that supports the health and growth of farmed fish is vital. When selecting alternative protein sources, producers must ensure they meet both quantity and nutritional requirements for aquaculture species. When feeds incorporating single-cell proteins are formulated to include all essential nutrients, fish can maintain good growth rates and feed efficiency without relying too much on fishmeal and exploiting marine resources. On a final note, single-cell proteins stand ready as a viable solution for ensuring sustainable growth and supply stability that the aquaculture industry will need in the coming years.
References
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5Machuca C, Méndez‑Martínez Y, et al. Yeast β‑Glucans as Fish Immunomodulators: A Review. Animals. 2022;12(16):2154. https://doi.org/10.3390/ani12162154
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8Becker J, Rohles CM, Wittmann C. Metabolically engineered Corynebacterium glutamicum for bio-based production of chemicals, fuels, materials, and healthcare products. Metabolic Engineering. 2018;50:122–141. https://doi.org/10.1016/j.ymben.2018.07.008
9Chistoserdova L, Chen SW, et al. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol. 2003;185(10). https://doi.org/10.1128/jb.185.10.2980-2987.2003
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11Mensah DD, Montero R, et al. In vitro salmonid models as tools for studying microbial-derived immunostimulants and aquaculture relevant salmonids pathogens: Current status and future perspectives. Aquaculture. 2025;595:741695. https://doi.org/10.1016/j.aquaculture.2024.741695
12Sharma N. Feed Futures: Building Markets for Algae and Insects. Alternative feed ingredients in a world of more volatile fishmeal and fish oil supply. Presentation at: North Atlantic Seafood Forum 2025; 2025 Mar 4–6; Bergen, Norway
About Dr. Federico Melenchón Ramírez
With a PhD in aquaculture from the Autonomous University of Barcelona, Federico Melenchón Ramírez’s doctoral research focused on the valorization of insect meals as an alternative protein source to fishmeal. He is experienced in fish nutrition research and alternative proteins, with additional interests in sustainable production and circular economy. Ramírez is highly motivated by optimization processes that enhance production efficiency and reduce waste, such as in fish, microalgae, or bacteria and is also passionate about education, scientific communication, and emotional health.
