Single cell protein: production, advantages, and uses in aquaculture

Single cell protein (SCP) is presented as a promising and sustainable solution to the growing demand for proteins, with applications in both animal feed and human consumption (Li et al., 2024). Additionally, SCP has the potential to reduce the aquaculture industry‘s reliance on marine ingredients and soy protein, but it requires capital investment and collaboration across the value chain to achieve large-scale sustainable production (Ellahi y Firdous, 2023).

In this article, we present the definition of single-cell protein, the different types that exist, the production process, its advantages and disadvantages, its use in aquaculture species’ feed, and the challenges that need to be overcome for it to become an alternative to traditional aquaculture feed ingredients.

What is Single cell Protein?

The term single-cell protein (SCP), also known as microbial protein, refers to proteins produced by microorganisms such as bacteria, yeasts, fungi, and single-celled algae. These proteins, cultivated through biotechnological processes, are considered a sustainable source of nutrients for both humans and animals. The ability of these microorganisms to grow in controlled conditions makes them an attractive option compared to conventional proteins derived from plants or animals.

Single-cell Protein Production: Processes and Sources

The production of single cell protein involves cultivating microorganisms on specific substrates, which can include agricultural residues, industrial by-products, or even carbon emissions. This process not only reduces waste but also generates protein-rich biomass.

Single cell Protein Production Process

The process of producing single-cell protein (SCP) involves several stages, from strain selection to the distribution of SCP products to end-users. Below is a detailed breakdown of the process, based on scientific literature:

Strain Selection

Microorganisms such as bacteria, yeasts, fungi, or microalgae are selected for their rapid growth and high protein content. Common species used include Methylobacterium, Candida utilis, Chlorella, Spirulina, Fusarium venenatum, and several methane-oxidizing bacteria.

Substrate Preparation

Substrate preparation is a crucial step in single cell protein production as it converts substrates into a usable carbon source. Substrates can vary, including high-energy sources (such as methane and methanol), organic waste, and renewable plant sources. Sharif et al., (2021) cite examples of substrates such as apple pomace, cassava peels, citrus pulp, potato peels, and pineapple waste.

Preparation methods vary depending on the substrate and include:

• Wet Preparation: For substrates with high moisture content, such as fruit and vegetable residues. This includes washing with water or acid, pulverization, and filtration.
• Dry Preparation: Used for drier materials like agricultural waste, which may require grinding and enzymatic treatment to enhance nutrient accessibility.

Pre-treatments with acids, alkalis, or steam have also been investigated to improve access to cellulose in lignocellulosic substrates. It is also important to note that substrates must be non-toxic, abundant, renewable, inexpensive, and capable of supporting rapid microbial growth.

Fermentation

Production takes place in bioreactors where microorganisms are fed substrates such as molasses, hydrocarbons, or nitrogen compounds. Fermentation can be aerobic or anaerobic, depending on the organism used. Li et al. (2024) describes the following fermentation processes:

• Solid-state fermentation (SSF): Conducted on a solid substrate without free liquid phase, ideal for filamentous fungi and some yeasts.
• Liquid-state fermentation (LSF): Microorganisms are cultured in a continuous liquid substrate with a high water content, allowing precise control over parameters such as temperature, pH, and oxygen supply.
• Semi-solid fermentation: An intermediate method between SSF and LSF, where liquid content is increased to improve nutrient and oxygen distribution.

Gaseous fermentation is an innovative method using gases like CO, CO2, or H2 as substrates for biomass production. Traditional fermentation, a spontaneous process involving the natural growth of microorganisms, is also practiced.

Harvesting and Processing

Once fermentation is complete, microbial biomass is harvested. Protein recovery after harvesting involves different cell disruption methods to release intracellular proteins:

• Mechanical methods: sonication, ball milling, high-pressure homogenization, and microfluidization.
• Chemical methods: alkaline treatment, acid treatment, and chaotropic agents.
• Biological methods: enzymes such as lysozyme, cellulase, and proteases.

For animal feed, after protein recovery, concentration is achieved through dehydration, precipitation, ultrafiltration, spray drying, and lyophilization. However, if single-cell protein is to be used for human consumption, additional processing steps are required to ensure product safety and quality.

Optimization and Control

Metabolic engineering approaches are being developed to improve productivity, yield, and protein quality. This includes optimizing metabolic pathways for the production of high-quality proteins.

Omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metametabolomics are also employed to understand cell interactions and improve stability and productivity.

Production methods

The choice of production method depends on several factors, including the type of microorganism, the available substrates, and the operating conditions. Ye et al., (2024) report that there are different production scenarios that are classified according to the energy source (phototrophic or chemotrophic) and the carbon substrates (autotrophic or heterotrophic) used:

Heterotrophic processes

These processes use organic carbon sources such as glucose, which is obtained from the hydrolysis of cellulosic sugar streams and agricultural waste. Methane, derived from anaerobic digestion or natural gas extraction, is also used.

• Main challenge: The raw material pretreatment is costly and requires a lot of energy. The hydrolysis of lignocellulosic biomass is a significant bottleneck.

Autotrophic processes

These processes use inorganic carbon, specifically CO2, and energy is obtained from light (photoautotrophic) or from chemical compounds such as H2 (chemoautotrophic).

• Main challenge: Limited fermentation due to low mass transfer of gaseous substrates and cell harvesting.

Examples of single cell protein

It is important to highlight that the choice of microorganism and substrate depends on factors such as cost, availability, conversion efficiency, and the desired nutritional profile of the unicellular protein. Some notable examples in unicellular protein production include:

Microalgae

• Arthrospira platensis (spirulina): Cultivated in saline and alkaline waters, it is used as a food coloring, biofertilizer, and functional food ingredient (Li et al., 2024). It has a high protein content (60%) and is one of the most commercially marketed SCP products (Pereira et al., 2022).
• Chlorella sp., Dunaliella sp.: These species are also important sources of unicellular protein (Rashid et al., 2024). Chlorella is a genus of unicellular green algae used as a nutritional supplement due to its high protein, lipid, and other nutrient content (Li et al., 2024).

Bacteria

• Methylobacterium spp.: These bacteria are used to produce SCP from C1 carbon compounds like methane and methanol (Gundupalli et al., 2024). Methylobacterium extorquens is used as an SCP source for Atlantic salmon feed (Salze y Tibbetts, 2021). Other methanotrophic bacteria like Methylococcus capsulatus are also used. Woolley et al., (2023) reported that SCP derived from Methylococcus capsulatus is a viable and effective substitute for up to 75% of fishmeal in barramundi (Lates calcarifer) diets.
• Clostridium spp.: Used in the production of ProTyton, an SCP product with 85% protein content, used for feeding Atlantic salmon and shrimp (Pereira et al., 2022).
• Purple non-sulfur bacteria: These bacteria can be used for wastewater treatment and simultaneous SCP production. Rhodopseudomonas palustris is one of the purple non-sulfur bacteria used in SCP production.
• Corynebacterium ammoniagenes: The digestibility of amino acids from its SCP in growing pigs has been demonstrated.

Yeasts

• Candida utilis: This yeast is cultivated on various substrates like potato processing waste, soybean molasses, and food industry waste for unicellular protein production (Ye et al., 2014). It is also used in the production of protein from beer brewing residues.
• Saccharomyces cerevisiae: This yeast is used to produce SCP from various sources, including fruit waste and agricultural byproducts.
• Yarrowia lipolytica: This yeast is used for unicellular protein production from agro-industrial waste. It has potential to produce lipids and proteins from different carbon sources, including inulin.

Fungi

• Fusarium venenatum: This fungus is used to produce Quorn™ mycoprotein, a product marketed for human consumption since 1985. Filamentous fungi can have a high protein content, although part of it may be in the form of cell wall components (Li et al., 2024). Aspergillus oryzae has also been studied for unicellular protein production.

Protists

• Schizochytrium limacinum: This protist is of interest for its ability to produce omega-3 fatty acids (Jones et al., 2020).

Applications of unicellular protein: Animal and human feed

The application of unicellular protein spans various fields, with feed being one of the primary areas of impact. According to Bratosin et al., (2021), the main applications of unicellular proteins are:

• Animal feed: SCP is used in animal feed and nutrition for fattening poultry, laying hens, calves, and pigs. It can replace more expensive protein sources like fishmeal and soybean products.
• Food additives: Unicellular protein is used as a carrier for vitamins and flavors, and as an emulsifier to improve the nutritional value of baked goods, prepared meals, and soups. It is also used as starter cultures in bread, beer, and wine production.
• Industrial processes: single cell protein is used as a foam stabilizer and in paper and leather processing.
• Food production: Unicellular protein can be used as a meat substitute to address food shortages and hunger. It is also used as an ingredient in vegetarian foods and as a seasoning.
• Aquaculture: Yeast-derived single cell protein is used in aquaculture diets as a partial replacement for fishmeal due to its nutritional profiles and large-scale production. It is also applied for fortifying unsaturated fatty acids in Artemia and rotifers.

Advantages vs Disadvantages of single cell protein

The following table summarizes the main advantages and disadvantages of single cell protein, highlighting both its potential and challenges for mass adoption.

Comparative table of the advantages and disadvantages of single-cell protein (SCP).

Differences Between Microbial Protein and Other Types of Single-Cell Protein

Although often used interchangeably, the term microbial protein can refer exclusively to proteins derived from microorganisms such as bacteria and fungi. On the other hand, single cell protein also includes single-celled algae. These differences reflect their origin and specific applications.

Uses of Single Cell Proteins in Aquaculture

According to Pereira et al. (2022), single cell protein has several promising applications in the aquaculture industry, primarily as a substitute for conventional protein sources in fish and other aquatic animal feed. Similarly, Jones et al. (2020) report having conducted extensive feeding trials with aquaculture species such as white shrimp (Litopenaeus vannamei), Atlantic salmon (Salmo salar), and rainbow trout (Oncorhynchus mykiss).

In this regard, single cell protein (SCP) offers several important benefits for aquaculture food production, which can be grouped as follows:

• High Protein Content: Single cell protein has a high protein level, which can reach up to 80% on a dry weight basis, making it an attractive alternative to traditional protein sources. In comparison, some microalgae can contain up to 70% protein, and fungi range from 30% to 50%. Gundupalli et al. (2024) report that bacterial single cell protein (BSCP) production from species of Methylobacterium (Methylophilus methylotrophus and Methylococcus capsulatus) is a sustainable alternative to traditional protein sources.
• Favorable Amino Acid Profile: Single cell protein contains a good amino acid profile, including essential amino acids such as lysine, methionine, and threonine, which are needed for fish growth and development. In some cases, the amino acid profile of single cell protein is comparable to that of fishmeal, a commonly used protein source in aquaculture.
• Pigment Production: Some microalgae, such as Spirulina pacifica and Haematococcus pluvialis, can enhance the color of fish flesh, which is an important factor for quality and consumer acceptance. On the other hand, Rashid et al. (2024) report that purple non-sulfur bacteria (PNSB) carotenoids protect fish from diseases.
• Sustainable Production: The production of single cell protein can be more sustainable than other protein sources as it requires less land and water, and its production is not dependent on climatic variations. Moreover, SCP can be produced using a wide variety of low-cost substrates, including agricultural and industrial waste, contributing to the circular economy.
• Rapid Production: The microorganisms used to produce single-cell protein have a fast growth rate, allowing for more efficient protein production compared to other sources. Bacteria, for example, can multiply in as little as 20 to 120 minutes.
• Versatility: SCP can be produced by a variety of microorganisms, including bacteria, algae, fungi, and yeasts, allowing flexibility in the selection of the protein source. Furthermore, single-cell protein can be produced from various substrates, including inexpensive sugars and C1 carbon compounds.
• Reduced Antigens: Unlike plant proteins like soy meal, SCP does not contain antigens that may interfere with amino acid absorption in fish.
• Additional Benefits: SCP can provide additional benefits to fish, such as improved immune function, better gut health, and greater disease resistance. Additionally, single-cell protein may contain vitamins, phospholipids, and other functional compounds.
• Lower Carbon Footprint: The production of SCP in closed and controlled bioreactors generates fewer greenhouse gas emissions, although the environmental benefits are still being explored.

Salmon Feeding

Jones et al. (2020) reported that yeasts Candida utilis and Kluyveromyces marxianus can replace up to 40% of fishmeal in salmon diets without affecting performance; and that single-cell protein products based on methanotrophs have shown improved growth and feed efficiency in Atlantic salmon.

On the other hand, Tibbetts et al., (2025) concluded that single cell protein (SCP) meals derived from the natural strain of Methylovorus menthalis (strain J25) are promising for salmonid feeding applications (Salmo salar) due to their adaptability for large-scale production via continuous aerobic fermentation using low-cost C1 methanol.

Feeding Rainbow Trout with Single-Cell Proteins

Buttle et al.,(2024) reported that single-cell protein products can replace up to 20% of traditional ingredients (fishmeal and soybean meal) in rainbow trout (Oncorhynchus mykiss) feed without compromising growth and fish health. Similarly, Zamani et al., (2020) stated that rainbow trout fry fed diets where 25% and 50% of fishmeal were replaced with bacterial SCP were 9.1% and 21.8% heavier, respectively, than those fed the control diet.

Ruiz et al., (2023) concluded that bacterial single-cell protein (BSCP) derived from methanotrophic bacteria can be incorporated into aquaculture compound feeds to reduce the use of traditional fishmeal. They fed juvenile rainbow trout a diet with 50% replacement of fishmeal by BSCP and reported better growth and lower FCR values compared to the control group; in addition, disease resistance improved in juvenile rainbow trout when challenged with Aeromonas salmonicida subsp. salmonicida.

Feeding Marine Shrimp with SCP

Hamidoghli et al., (2019) reported that single cell protein extracted from Corynebacterium ammoniagenes (PRO) may be recommended as a source of single-cell protein for shrimp feeding, offering a cost-effective and underutilized alternative to fishmeal. The optimal PRO level as a replacement for fishmeal is between 10% (PRO2) and 20% (PRO4) without additional amino acid supplementation.

Jones et al. (2020) highlighted that in shrimp diets, several yeasts have successfully replaced fishmeal or soybean meal, with up to 50% C. utilis showing no adverse effects and even greater growth rates.

Challenges to Overcome for Single Cell Protein Production

The main challenges in harnessing single cell protein include aspects related to production, nutritional quality, safety, consumer acceptance, and economics.

Production Challenges

• Scalability: Despite the potential of SCPs, their large-scale production is still under development and limited. Large bioreactors and optimized processes are needed to achieve industrial production volumes.

• Costs: The production of single cell protein remains costly compared to conventional protein sources such as soy or fishmeal. High substrate, processing, and purification costs pose economic obstacles.

• Raw Material Pretreatment: Heterotrophic processes that use organic waste as substrates require pretreatment to increase sugar accessibility and availability for fermentation, which can be costly and energy-intensive. Emerging technologies aim to reduce these costs and environmental toxicity.

• Fermentation and Harvest Efficiency: For autotrophic processes, optimizing fermentation for higher yields and harvest efficiency are significant challenges. Methods such as bioflocculation and biofilm growth can reduce harvest costs.

• Stability of Mixed Cultures: The use of mixed cultures can enhance productivity and reduce operational costs, but maintaining the stability of these microbial communities over long periods is a challenge.

Challenges in Nutritional Quality

• Nucleic Acid Content: SCPs have a high nucleic acid content, which can increase uric acid in the blood serum and cause issues such as kidney stones in humans. Processing methods are required to reduce these compounds in products intended for human consumption.

• Digestibility: The cell wall of SCPs may be difficult for animals and humans to digest, limiting nutrient availability. Methods such as cell disruption can improve the digestibility of SCPs.

• Amino Acid Balance: Some SCPs may be deficient in certain essential amino acids, such as methionine and cysteine, requiring supplementation in animal and human diets.

• Fatty Acid Profile: SCPs may lack the essential fatty acids found in fishmeal, so supplementation should be considered in aquaculture diets.

Safety Challenges

• Toxins: Some strains of microorganisms can produce toxins (endotoxins, mycotoxins), requiring process optimization and aseptic techniques.

• Active Microorganisms: Consuming unprocessed single cell protein with active microorganisms can cause infections and gastrointestinal issues.

• Allergic Reactions: Some individuals may be allergic to certain types of single cell protein.

Consumer Acceptance Challenges

• Taste and Texture: SCPs can have flavors and textures that are unappealing to consumers, making their incorporation into human food difficult. Texturization technologies are needed to improve sensory properties.

• Perception: There is a negative perception regarding the use of microorganisms in food production, making consumer acceptance difficult.

Economic Challenges

• Price Competitiveness: SCPs must be price-competitive with other protein sources such as soy and fishmeal.

• Investment: Transitioning to large-scale commercial production requires significant investments in infrastructure, technology, and process optimization.

Overcoming these challenges is essential to fully harness the potential of SCPs as a sustainable and nutritious alternative to conventional proteins for human and animal feed.

Conclusion

Single-cell proteins (SCP) are a versatile product with a wide range of applications, from human and animal nutrition to industrial processes. Their potential as a sustainable protein source makes them an attractive alternative to address food and environmental challenges.

The future of single cell protein is promising. With advances in biotechnology and fermentation, production is expected to become more efficient and less costly. Additionally, its role in the circular economy and global food security could establish it as a key solution for a growing world. However, more research is needed to address the technical and consumer perception challenges associated with its production and application (Koukoumaki et al., 2024).

References

Bratosin, B. C., Darjan, S., & Vodnar, D. C. (2021). Single Cell Protein: A Potential Substitute in Human and Animal Nutrition. Sustainability, 13(16), 9284. https://doi.org/10.3390/su13169284

Buttle, L., Noorman, H., Roa Engel, C., & Santigosa, E. (2024). Bridging the protein gap with single-cell protein use in aquafeeds. Frontiers in Marine Science, 11, 1384083. https://doi.org/10.3389/fmars.2024.1384083

Ellahi, B. and Firdous, A. 2023. Single Cell Protein: Microbial Protein for Sustainable Aquaculture Feed and Nutrition. Chronicle of Aquatic Science 1(5): 18-28.

Gundupalli, M. P., Ansari, S., Vital da Costa, J. P., Qiu, F., Anderson, J., Luckert, M., & Bressler, D. C. (2024). Bacterial single cell protein (BSCP): A sustainable protein source from methylobacterium species. Trends in Food Science & Technology, 147, 104426. https://doi.org/10.1016/j.tifs.2024.104426

Hamidoghli, A., Yun, H., Won, S. et al. Evaluation of a single-cell protein as a dietary fish meal substitute for whiteleg shrimp Litopenaeus vannamei. Fish Sci 85, 147–155 (2019). https://doi.org/10.1007/s12562-018-1275-5

Jones, S. W., Karpol, A., Friedman, S., Maru, B. T., & Tracy, B. P. (2020). Recent advances in single cell protein use as a feed ingredient in aquaculture. Current Opinion in Biotechnology, 61, 189-197. https://doi.org/10.1016/j.copbio.2019.12.026

Koukoumaki, D. I., Tsouko, E., Papanikolaou, S., Ioannou, Z., Diamantopoulou, P., & Sarris, D. (2024). Recent advances in the production of single cell protein from renewable resources and applications. Carbon Resources Conversion, 7(2), 100195. https://doi.org/10.1016/j.crcon.2023.07.004

Li, Y. P., Ahmadi, F., Kariman, K., & Lackner, M. (2024). Recent advances and challenges in single cell protein (SCP) technologies for food and feed production. Npj Science of Food, 8(1), 1-25. https://doi.org/10.1038/s41538-024-00299-2

Pereira, A. G., Fraga-Corral, M., Garcia-Oliveira, P., Otero, P., Soria-Lopez, A., Cassani, L., Cao, H., Xiao, J., Prieto, M. A., & Simal-Gandara, J. (2022). Single-Cell Proteins Obtained by Circular Economy Intended as a Feed Ingredient in Aquaculture. Foods, 11(18), 2831. https://doi.org/10.3390/foods11182831

Rashid, N., Onwusogh, U. & Mackey, H.R. Exploring the metabolic features of purple non-sulfur bacteria for waste carbon utilization and single-cell protein synthesis. Biomass Conv. Bioref. 14, 12653–12672 (2024). https://doi.org/10.1007/s13399-022-03273-8

Ruiz, A., Sanahuja, I., Thorringer, N. W., Lynegaard, J., Ntokou, E., Furones, D., & Gisbert, E. (2023). Single cell protein from methanotrophic bacteria as an alternative healthy and functional protein source in aquafeeds, a holistic approach in rainbow trout (Oncorhynchus mykiss) juveniles. Aquaculture, 576, 739861. https://doi.org/10.1016/j.aquaculture.2023.739861

Salze, G. P., & Tibbetts, S. M. (2021). Apparent digestibility coefficients of proximate nutrients and essential amino acids from a single-cell protein meal derived from Methylobacterium extorquens for pre-smolt Atlantic salmon (Salmo salar L.). Aquaculture Research, 52(12), 6818–6823. https://doi.org/10.1111/are.15526

Sharif, M., Zafar, M. H., Aqib, A. I., Saeed, M., Farag, M. R., & Alagawany, M. (2021). Single cell protein: Sources, mechanism of production, nutritional value and its uses in aquaculture nutrition. Aquaculture, 531, 735885. https://doi.org/10.1016/j.aquaculture.2020.735885

Tibbetts, S. M., Piercey, M. J., Patelakis, S. J., & Stratton, B. (2025). Single-cell protein (SCP) meals from Methylovorus menthalis as feed ingredients for freshwater Atlantic salmon (Salmo salar L.): Digestibility, growth performance, nutrient utilization, and fish health. Aquaculture, 598, 741874. https://doi.org/10.1016/j.aquaculture.2024.741874

Woolley, L., Chaklader, M. R., Pilmer, L., Stephens, F., Wingate, C., Salini, M., & Partridge, G. (2023). Gas to protein: Microbial single cell protein is an alternative to fishmeal in aquaculture. Science of The Total Environment, 859, 160141. https://doi.org/10.1016/j.scitotenv.2022.160141

Ye, L., Bogicevic, B., Bolten, C. J., & Wittmann, C. (2024). Single-cell protein: Overcoming technological and biological challenges towards improved industrialization. Current Opinion in Biotechnology, 88, 103171. https://doi.org/10.1016/j.copbio.2024.103171

Zamani, A., Khajavi, M., Nazarpak, M. H., & Gisbert, E. (2020). Evaluation of a Bacterial Single-Cell Protein in Compound Diets for Rainbow Trout (Oncorhynchus mykiss) Fry as an Alternative Protein Source. Animals, 10(9), 1676. https://doi.org/10.3390/ani10091676