Alternative protein allergenicity is a growing concern as plant-based proteins, algae and microalgae, mycoproteins and insects enter mainstream diets. A recent review in the Journal of Agricultural and Food Chemistry (Günal-Köroğlu et al., 2025) examines the immune mechanisms driving food allergenicity and outlines processing strategies to reduce risks while preserving nutritional quality and safety. The rapid expansion of the alternative protein sector — fuelled by population growth, shifting dietary preferences, and the demand for sustainable food systems — brings both opportunities and technological challenges.
Effective allergen mitigation strategies are now essential for market acceptance, regulatory compliance, and consumer safety. For industry, allergenic risks pose significant market barriers, making the development of reduction protocols that maintain product quality and economic viability a priority. For science, the challenge lies in advancing the understanding of complex immune responses and creating evidence-based solutions for novel proteins that existing regulations do not fully address.
Background and significance of alternative protein allergenicity
Scientific understanding of allergenic mechanisms
Food allergies represent a substantial public health concern, affecting approximately 90% of allergic reactions through the ‘Big Eight’ allergens: cereals containing gluten, crustaceans, eggs, fish, milk, tree nuts, peanuts, and soybeans (Günal-Köroğlu et al., 2025). The FASTER Act has subsequently established sesame as the ninth major food allergen, in the United States, while the European Union recognises 14 allergens under EU law. The emergence of alternative proteins introduces additional complexity to allergenicity assessment, as current risk evaluation frameworks inadequately predict sensitisation to novel or processed proteins.
The immune system’s response to food allergens involves complex mechanisms, primarily mediated through IgE antibodies that trigger immediate hypersensitivity reactions ranging from mild discomfort to severe anaphylaxis. The structural characteristics of proteins, particularly the presence of specific allergenic epitopes recognised by the immune system, play a crucial role in determining allergenicity. These epitopes can be linear (continuous amino acid sequences) or conformational (dependent on protein folding), with linear epitopes retaining allergenicity even after processing, whilst conformational epitopes may lose their immunogenic potential.
Industry challenges and market requirements
Food manufacturers face increasing pressure to develop alternative protein products that meet stringent safety standards while satisfying consumer expectations for taste, texture, and nutritional value. The industry’s challenge lies in developing cost-effective processing strategies that can reliably reduce allergenicity across diverse protein sources without requiring prohibitively expensive infrastructure investments or compromising production efficiency.
Regulatory compliance demands comprehensive allergen risk assessment protocols, necessitating standardised technological approaches that can be validated through reproducible testing methodologies.
Supply chain integration requires processing technologies that can be seamlessly incorporated into existing manufacturing workflows without disrupting production schedules or quality control systems. Industry stakeholders increasingly seek versatile processing platforms capable of addressing multiple protein sources through adaptable parameter optimisation, reducing the need for protein-specific equipment investments whilst maximising operational flexibility.
Advanced analytical approaches
The comprehensive review included multiple analytical techniques to assess allergenicity across alternative protein sources. Classical methods including immunological assays (ELISA, Western blotting), clinical assessments (Skin Prick Test, Oral Food Challenge), and physicochemical analyses were utilised to evaluate IgE reactivity and immune system recognition of specific proteins (Günal-Köroğlu et al., 2025).
Advanced omics technologies and bioinformatics approaches were increasingly employed to complement traditional allergen assessment, including proteomics, genomics, and metabolomics for identifying and characterising allergenic proteins.
Bioinformatics tools such as AllerTOP, AlgPred, and AllergenPro were utilised to predict potential IgE-binding epitopes by analysing sequence motifs and structural characteristics. Molecular docking and dynamics simulations provided detailed insights into binding affinity and structural changes induced by chemical treatments, whilst sequence alignment tools identified homologous regions between novel proteins and known allergens to assess cross-reactivity risks.
Alternative protein sources and their allergenic profiles
Legumes: complex structures requiring targeted solutions
Legume proteins present significant allergenic challenges due to their complex protein structures, including storage proteins (cupin and prolamin superfamilies), profilins, and pathogenesis-related proteins. From an industry perspective, legume processing technologies require sophisticated approaches to address these complex allergenic protein structures whilst maintaining functionality essential for product formulation.
Soybean proteins can cause severe allergic reactions including urticaria, rhinitis, and anaphylactic shock. Thermal treatments of boiling and autoclaving demonstrated promising results, with allergenicity reductions of 43-59% through boiling at 100°C and 82-83% with autoclaving at 121°C for 20 minutes, highlighting autoclaving as more effective due to epitope destruction and structural changes (Pi et al., 2022). Industrial thermal processing systems incorporating these parameters offer manufacturers proven methodologies with well-understood scale-up characteristics.
White bean byproducts showed persistent immunoreactivity following enzymatic hydrolysis, likely due to antinutritional factors hindering protein digestion, requiring manufacturers to develop multi-stage processing approaches (Calcinai et al., 2022).
Mung bean (Vigna radiata L.) contains allergenic storage proteins including globulins, albumins, and legumins, with enzymatic hydrolysis via papain, alcalase, and flavorzyme demonstrating variable effectiveness in allergenicity reduction (Calcinai et al., 2023). Industrial applications of these enzymes require careful optimisation of processing parameters to achieve maximum allergen reduction whilst preserving protein solubility and functional properties.
Cereals: gluten challenges and processing innovations
Cereal proteins, classified by solubility into albumins, globulins, and prolamins (gliadin and glutenin), present varying allergenic potential requiring sophisticated technological interventions. Wheat contains 28 identified allergens, with α-amylase inhibitors linked to baker’s asthma and wheat hypersensitivity, whilst prolamins, particularly ω-5 gliadin, trigger wheat-dependent exercise-induced anaphylaxis (Günal-Köroğlu et al., 2025).
Advanced cereal processing technologies address complex gluten-related challenges through multi-modal treatment approaches:
- sourdough fermentation systems demonstrated effectiveness in reducing α-trypsin inhibitor levels by 41%, offering manufacturers natural processing approaches that align with consumer preferences for minimally processed foods (Boakye et al., 2022). Industrial fermentation protocols combined with enzymatic treatments achieved the greatest reduction in immunogenicity compared to individual methods, providing manufacturers with synergistic processing solutions;
- high-pressure processing and pulsed electric field technologies offer manufacturers innovative approaches to cereal allergen modification through non-thermal mechanisms that preserve nutritional content whilst achieving substantial allergenicity reductions. These technologies enable selective protein modification without the thermal damage associated with conventional processing methods.
Tree nuts and oilseeds: stability challenges and chemical solutions
Tree nut allergens demonstrate exceptional stability, resisting heat and digestive enzyme degradation, requiring robust technological interventions for effective allergen reduction. Cashew nuts contain key allergens Ana o 1, Ana o 2, and Ana o 3, with Ana o 3 linked to severe reactions and used as a clinical allergy predictor (Günal-Köroğlu et al., 2025). Industrial thermal treatments including boiling, autoclaving, and pressured heating combined with enzymatic hydrolysis showed significant allergenicity reduction, with complete elimination of protein bands observed after autoclaving and pressured heating.
Chemical modification strategies using polyphenol interactions demonstrate considerable promise for industrial applications. Apple polyphenols significantly reduced peanut allergenicity by binding to proteins, with epicatechin proving most effective, followed by catechin, chlorogenic acid, rutin, and phlorizin in decreasing IgE, IgG1, histamine, and inflammatory markers (Sun et al., 2023). Industrial-scale polyphenol application demonstrates significant potential for allergen reduction whilst providing additional antioxidant benefits that enhance product shelf-life and nutritional value.
Emerging protein sources: novel challenges and innovative solutions
Algae and microalgae
Algae and microalgae are one of the most promising alternative protein sources, particularly microalgae which were the focus of the ProFuture research project funded by the Horizon 2020 programme. From the perspective of protein quality (digestibility and essential amino acid content), optimal value has been demonstrated even when added to various preparations (e.g. vegetable soups), but they are not exempt from allergenicity risks due precisely to their significant protein concentration.
Microalgae-derived proteins, particularly from Spirulina and Chlorella, have been associated with allergic reactions including anaphylaxis. The allergenic protein C-Phycocyanin Beta Subunit (15-35 kDa) in Spirulina represents a significant concern for food manufacturers.
Algae processing technologies address these specific challenges through targeted thermal and enzymatic treatments that reduce allergenicity whilst preserving valuable nutritional and functional properties (Bianco et al., 2022).
Biorefinery integration enables manufacturers to optimise allergen reduction within comprehensive protein extraction and purification processes.
Mycoproteins
Mycoproteins, primarily derived from Fusarium venenatum, have received considerable attention as sustainable protein alternatives, however their allergenic potential remains a concern due to cross-reactivity with fungal allergens and mould proteins, primarily of the genera Fusarium, Cladosporium, Aspergillus and Alternaria.
Although generally considered safe, some components of mycoproteins can trigger immune responses in susceptible individuals. High-molecular-weight proteins in mycoproteins may be recognized by the human immune system, increasing their allergenic potential. Additionally, specific fungal proteins such as enolase and triose-phosphate isomerase have been identified as cross-reactive allergens, meaning individuals sensitized to airborne fungi or other fungal allergens may experience adverse reactions to mycoprotein consumption (Hoff et al., 2003).
Edible insects
The European Food Safety Authority (EFSA) has evaluated several insect species for authorisation as novel foods within the European Union. The following insects have been approved — often with mandatory warnings advising individuals allergic to crustaceans, molluscs, and dust mites to avoid consumption — or are currently under assessment:
- Tenebrio molitor (yellow mealworm) is authorised, with a further dossier under evaluation for a protein-rich powder;
- Locusta migratoria is authorised, with another application under examination;
- Acheta domesticus (house cricket) is authorised, with other applications under EFSA examination;
- Alphitobius diaperinus (lesser mealworm beetle) is authorised, but under evaluation for a new application relating to a protein powder;
- Hermetia illucens (black soldier fly) is likewise authorised but under evaluation for a new application;
- on the other hand, novel food applications for Gryllodes sigillatus (banded cricket) and Apis mellifera (honeybee) have been withdrawn.
Edible insects pose specific allergenic risks due to cross-reactivity with crustacean allergens, primarily from shared proteins such as tropomyosin and arginine kinase. Insect protein processing therefore requires specialised technological approaches to address cross-reactivity concerns while preserving the unique nutritional benefits of these proteine. Thermal processing methods, including boiling, frying, and microwave treatment, can reduce cross-reactivity with shrimp and house dust mite allergens, though effectiveness varies by species and treatment conditions (Lamberti et al., 2021).
Comprehensive processing technologies for allergenicity reduction
Thermal processing: precision engineering for industrial applications
Industrial thermal processing represents the most established technological approach for allergen mitigation, offering manufacturers proven methodologies with well-understood scale-up characteristics. Autoclaving technologies consistently demonstrate superior allergenicity reduction compared to conventional thermal treatments, achieving over 80% reductions across multiple protein sources whilst maintaining industrial processing speeds (Günal-Köroğlu et al., 2025). Process optimisation through precise temperature and time control enables manufacturers to achieve maximum allergen reduction whilst preserving essential nutritional and functional properties.
Advanced thermal systems including microwave processing, ohmic heating, and radiofrequency treatments offer enhanced processing control and energy efficiency compared to conventional methods. These technologies enable selective protein modification through controlled heating rates and temperature profiles, allowing manufacturers to target specific allergenic epitopes whilst preserving desirable protein functionalities essential for product performance. Thermal processing works through protein denaturation and epitope disruption, with effectiveness varying significantly based on protein stability and processing conditions.
Enzymatic hydrolysis: targeted and scalable solutions
Enzymatic hydrolysis systems provide manufacturers with highly controllable tools for targeted allergen reduction through specific protein cleavage mechanisms. Industrial enzyme applications utilising papain, alcalase, and flavorzyme demonstrate effectiveness across multiple protein matrices, with process parameters readily adaptable to different production scales and protein concentrations (Calcinai et al., 2023). Optimised hydrolysis protocols enable manufacturers to achieve substantial allergenicity reductions whilst maintaining protein solubility, emulsification capacity, and other functional properties critical for product formulation.
Enzymatic hydrolysis utilises proteolytic enzymes to cleave allergenic proteins into smaller peptides and amino acids, disrupting both conformational and linear IgE-binding epitopes. Enzyme reactor design and process integration allow manufacturers to incorporate enzymatic treatments into continuous production lines, minimising processing time and reducing operational costs. Multi-enzyme systems offer enhanced processing flexibility, enabling simultaneous targeting of multiple allergenic proteins through complementary cleavage mechanisms whilst optimising overall processing efficiency.
Chemical modification: innovation in molecular engineering
Polyphenol conjugation technologies represent an emerging frontier in allergen mitigation, offering manufacturers innovative approaches to allergenicity reduction through protein cross-linking and epitope masking mechanisms. Polyphenol-induced modifications provide innovative approaches to allergenicity reduction through protein cross-linking and structural changes. Polyphenols including chlorogenic acid, catechin, and tannins interact with allergenic proteins to reduce IgE-binding capacity through epitope masking and protein aggregation.
Glycation processing systems use controlled Maillard reactions to modify protein structures and reduce allergenicity by disrupting epitopes. These industrial processes provide scalable solutions that not only mitigate allergens but also enhance flavour development and browning characteristics, suited to specific product applications. However, careful control is required to prevent the formation of new allergenic epitopes (Günal-Köroğlu et al., 2025).
Synergistic processing approaches: maximising efficacy
Multistage processes integrating thermal, enzymatic, and chemical treatments achieve greater allergenicity reduction than individual methods, providing comprehensive solutions for complex protein matrices. Specifically, combining thermal treatment with enzymatic hydrolysis followed by chemical modification delivers optimal results while preserving protein functionality and nutritional quality.
Continuous processing technologies that incorporate multiple treatment modes ensure consistent allergen reduction at industrial scale, optimising processing times and energy consumption. The implementation of automated control systems enables precise monitoring and real-time adjustment of process parameters, guaranteeing reproducible allergen mitigation outcomes.
Finally, fermentation processes combined with enzymatic treatments show particular promise for cereal and legume proteins, broadening the scope of technological interventions for allergenicity reduction.
Future technological developments and research directions
Advanced processing technologies and industry innovation
Next-generation processing systems incorporating artificial intelligence and machine learning algorithms offer manufacturers unprecedented control over allergen reduction processes through predictive modelling and real-time optimisation capabilities.
Precision processing technologies enable targeted modification of specific allergenic epitopes whilst preserving overall protein functionality, representing a paradigm shift towards customised allergen mitigation strategies.
The development of precision allergen mitigation strategies depends on advances in key areas, notably the use of machine learning and artificial intelligence for enhanced epitope prediction and allergenicity assessment (Günal-Köroğlu et al., 2025).
Regulatory and implementation contexts
Regulatory frameworks require substantial updates to address the complexities associated with the allergenicity of novel proteins, as current systems — primarily focused on conventional allergens — leave significant gaps in the assessment of alternative proteins. Regulatory validation processes demand comprehensive documentation on processing efficacy and safety, requiring manufacturers to develop robust quality assurance protocols capable of demonstrating reliable and reproducible allergen reduction outcomes.
The creation of comprehensive allergen databases, incorporating alternative proteins and aligned with standardised nomenclature such as WHO/IUIS, is essential to ensure consistency in food safety risk assessments and to support regulatory decision-making. In parallel, personalised nutritional approaches could enable tailored dietary recommendations based on specific allergenic sensitivities to alternative proteins, integrating advanced diagnostic technologies with customised processing solutions.
Conclusions
The comprehensive analysis demonstrates that whilst alternative proteins present significant allergenic challenges, multiple effective processing strategies exist for allergenicity reduction, addressing both scientific understanding and industrial implementation requirements:
- thermal processing, particularly autoclaving, consistently achieves substantial allergenicity reduction across protein sources whilst offering manufacturers proven approaches with established scale-up characteristics;
- enzymatic hydrolysis offers targeted protein breakdown capabilities that can be readily integrated into existing production workflows whilst achieving substantial allergen reductions;
- chemical modification through polyphenol interactions provides innovative mitigation approaches that offer additional product benefits including enhanced antioxidant properties and improved shelf-life characteristics;
- combined processing approaches demonstrate superior allergenicity reduction compared to individual treatments, providing manufacturers with comprehensive solutions for challenging protein matrices.
Future research priorities should focus on optimising processing methods to ensure effective allergen reduction whilst maintaining nutritional quality and safety. The development of standardised assessment protocols for novel protein allergenicity represents a critical need for regulatory approval and consumer confidence.
Technology development initiatives must prioritise the development of versatile, cost-effective processing platforms that can address multiple protein sources whilst maintaining the functional properties essential for product development.
Regulatory harmonisation and international standards development will facilitate global market acceptance of alternative protein products whilst ensuring consistent safety outcomes.
Dario Dongo e Andrea Adelmo Della Penna
Cover art copyright © 2025 Dario Dongo (AI-assisted creation)
References
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Dario Dongo, lawyer and journalist, PhD in international food law, founder of WIISE (FARE - GIFT - Food Times) and Égalité.
Graduated in Food Technologies and Biotechnologies, qualified food technologist, he follows the research and development area. With particular regard to European research projects (in Horizon 2020, PRIMA) where the FARE division of WIISE Srl, a benefit company, participates.
