Producing plant-based compounds using microbes offers clear economic and environmental advantages over traditional chemical synthesis or extraction from plants. Despite early successes and a few products reaching the market, many valuable plant molecules—especially oxygen-rich oxygenated plant metabolites (OPMs)—remain difficult to produce. These compounds are typically made in nature by cytochrome P450 enzymes (CYPs), which are challenging to express and engineer in microbial systems, limiting access to many of these compounds.
At the same time, artificial intelligence (AI) and machine learning (ML) are advancing rapidly, yet their potential in engineering biology remains underused. The deCYPher project bridges this gap by developing a standardized AI/ML platform to unlock the microbial production of OPMs, making these high-value molecules more accessible for industrial and societal applications.
deCYPher builds an AI/ML pipeline that integrates across all stages of the Design-Build-Test-Learn (DBTL) cycle, and across the biotech value chain. This modular platform is combined with smart databases and synthetic biology tools to support innovation throughout the sector. Project activities begin at TRL 2–3, with a target of reaching TRL 5.
For OPM production, deCYPher focuses on three main objectives:
(1) discovering and selecting the right CYP enzymes;
(2) ensuring their proper expression and localization in microbial hosts; and
(3) optimizing the microbial chassis and overall bioprocess.
Alongside its technical work, deCYPher actively involves stakeholders—including industry, regulators, NGOs, and citizens—to reflect on the societal and ethical implications of integrating AI and SynBio.
The project’s pathway to impact covers four key areas:
(1) Scientific and technical impact – A generic, modular AI/ML pipeline is developed for every step of the DBTL cycle. This foundation supports the efficient and sustainable development of bioprocesses for flavonoids and terpenoids, and is adaptable across the life sciences.
(2) Economic impact – By using an integrated approach across the bioprocess development chain, the project enables scalable and competitive production of OPMs with broad applications, supporting economic valorization.
(3) Sustainability impact – The use of metabolically versatile microbial hosts supports improved resource use and the shift to non-fossil, local feedstocks, contributing to cost-effective and sustainable bioproduction.
(4) Societal impact – Through open and citizen science approaches, and by applying science anticipatory methods, deCYPher supports a deeper understanding of the societal implications of AI/ML in SynBio, ensuring alignment with stakeholder needs and the safe development of emerging biotechnologies.
