The way we produce meat today is destroying our planet, and without a sustainable alternative, the cost will be existential. The livestock farming industry is a major contributor to environmental degradation, responsible for approximately 14.5% of all greenhouse gas emissions^[1]. It drives biodiversity loss through deforestation and land-use conversion, while the extensive use of antibiotics in animal agriculture accelerates the spread of antimicrobial resistance^[2]. As the global population grows, the demand for protein will rise correspondingly, intensifying these pressures, forcing us to confront the urgent need for sustainable and nutritionally complete alternatives to conventional meat.

Cultivated meat has been presented as a promising solution due to its structural and nutritional similarity to traditional meat, providing a more natural alternative over plant-based substitutes. However, large-scale adoption remains limited by higher production costs, primarily associated with cell culture media and bioreactor scale-up^[3]. Cell culture media, which supplies the nutrients and signalling molecules required for cellular growth, includes expensive recombinant components such as growth factors. Scaling cultivated meat requires bioreactors of 200 to 20,000 L and demands substantial quantities of these expensive media, preventing cost parity with conventional meat^[3].

Techno-economic analyses consistently identify growth factors as the primary cost-drivers of cultivated meat production, contributing up to 70% of the total production costs^[4]. To make cultivated meat economically viable, it is essential to develop alternative, low-cost recombinant growth factor production systems. Our project addresses this challenge by engineering Komagataella phaffii (K. phaffii), also commonly referred to as Pichia pastoris, to produce growth factors more efficiently, increasing yields and simplifying downstream purification — a core determinant of production economics.

K. phaffii is a widely used strain in both academia and industry for recombinant protein production due to its well-characterised promoters, eukaryotic post-translational machinery, and high secretion efficiency. However, production inefficiencies arise from the secretion of exopolysaccharides (EPS), which co-purify with target proteins and increase purification costs^[5],[6],[7]. To mitigate this, we engineered a novel K. phaffii strain, Mannoless, designed to reduce EPS secretion by modulating key enzymes involved in mannose biosynthesis and cell wall formation. By aiming to alleviate EPS-associated downstream burdens and carbon waste, Mannoless improves growth factor yields and production prices.

Through this work, our goal is to accelerate the scalability of the cultivated meat industry by producing cost-effective recombinant growth factors, and advocating for sustainable, ethical food production.

Mannoless is our K. phaffii strain engineered to minimise exopolysaccharide (EPS) secretion, with the goal of freeing up more cellular energy for recombinant protein production and thereby increasing the yields of our proteins of interest. Specifically, we used a three-pronged strategy to target cell wall integrity and protein glycosylation pathways^[5].

Hoc1

The Hoc1 gene encodes a mannosyltransferase required for cell wall construction. Almost all industrial K. phaffii strains contain a single-base-pair deletion in Hoc1, resulting in a frameshift introducing a premature stop codon, presenting as a thinner cell wall. While this improves secretion and transformation efficiency, the disrupted linkage of cell wall mannose polymers causes free mannan polymers to be secreted instead, leading to EPS being detected alongside the recombinant protein.

Our goal is to restore and downregulate the original Hoc1 sequence to increase active site specificity and prevent EPS formation.

BioKernel is our dry lab software platform designed to optimise experimental design and strain engineering in synthetic biology. It applies Bayesian optimisation to guide biological experiments toward optimal outcomes using minimal resources. The framework was developed to address a key challenge of biological research, the high cost and limited throughput of experimental testing, by allowing researchers to systematically explore complex parameter spaces arising in biological experimentation without requiring coding expertise^[11],[12].

BioKernel can be downloaded from: https://gitlab.igem.org/2025/software-tools/imperial

Bayesian optimisation (BO) is a machine learning strategy that identifies optimal experimental conditions by iteratively learning from prior results. It constructs probabilistic models balancing exploration and exploitation, enabling efficient optimisation even in high-dimensional, noisy systems typical of biological research^[12],[13].

We developed BioKernel as a no-code, modular Bayesian optimisation framework tailored to biological experimentation. Its key features include:

• Modular kernel architecture adaptable to diverse biological datasets.
• Heteroscedastic noise modelling to handle variable experimental uncertainty.
• Flexible acquisition functions balancing exploration–exploitation trade-offs.
• Batch optimisation support for parallel experimental design.

Additionally, to validate our framework, we conducted two complementary tests. Retrospective analysis on published metabolic datasets demonstrated that BioKernel can reproduce known optima using significantly fewer experimental iterations than the original studies. The algorithm approached the optimal value within mean 0.2 normalised euclidean distance (maximum distance for 4 dimensions is 2) within an average of 19 iterations, compared to the 83 points investigated in literature. For prospective validation, we will apply our algorithm to optimise astaxanthin biosynthesis in E. coli Marionette strains^[14], which contain twelve orthogonal, genomically integrated sensors enabling precise multi-dimensional induction control.

BioKernel is the first iGEM software capable of performing advanced optimisation without requiring programming knowledge, bridging the gap between computational modelling and experimental design. By releasing BioKernel as an open-source tool, we aim to make rigorous, data-driven optimisation accessible to all experimental biologists, accelerating the path from design to discovery and enabling more efficient synthetic biology research worldwide.

Public understanding and trust in cultivated meat are still developing, and often shaped by confusion or skepticism toward synthetic biology. Our educational efforts aimed to strengthen trust in science, specifically synthetic biology within the public sphere, by demystifying the process behind innovation and encouraging open, nuanced discussions rather than simple promotion.

We explored how people perceive scientific innovation through public surveys on cultivated meat and trust in science, using these insights to guide every outreach material and event we designed. Our goal was to bring synthetic biology and alternative proteins into everyday conversation naturally through curiosity, dialogue, and reflection, while engaging all age categories.

We addressed the growing “techno-phobia” surrounding biotechnology by combining clear science communication with bioethical reflection. This approach encouraged critical and constructive engagement with the future of food and synthetic biology, promoting awareness of and trust in innovation.

Our Human Practices work guided the project’s direction at every stage, ensuring our science was socially aware, ethically grounded, and practically relevant. We conducted a broad investigation of the precision fermentation and cultivated meat ecosystem, covering academic progress, industrial bottlenecks, and the evolving market landscape.

Through expert consultations across academia, entrepreneurship, intellectual property, and industry, we gained insight into both the technical feasibility and societal impact of animal-free growth factors. This process not only informed our experimental design and process optimisation, but also made our team uniquely aware of industry-level precision fermentation, strain engineering, and protein manufacturing in yeast — as well as the regulatory and investment realities shaping the alternative protein field.

By engaging with diverse stakeholders, we built a project that not only addresses scientific and economic challenges but also reflects on the social responsibility and future implications of cultivated meat technology. These discussions helped us integrate ethical reflection and practical insight into every design decision.