Biomanufacturing and digital twins
The growth of the circular bioeconomy, or the commercial and industrial application of sustainable bio-based products and services, has long been an ambition for many governments, public and private stakeholders. The benefits of that economic system are manifold, especially for energy use reduction, increased innovation and sustainability.
Transitioning towards a system of production firmly rooted in biotechnological innovation, and away from traditional petroleum-based manufacturing practices, is dependent on the enabling research from fields such as synthetic biology, information technology, and industrial biotechnology.
Our mission & Strategy
We explore, develop and implement pioneering technologies that support bio-based production. We work across the full spectrum of biomanufacturing: from bioplastics to pharmaceuticals, and use digital twins to help us design and optimise these processes. These digital twins combine historical data with real-time process information to model and predict future performance. Our mission is to deliver excellent multidisciplinary research and education that advance both biomanufacturing and the use of digital twins.
Strategy
We specialize in applying microbial systems, advanced bioengineering and modelling technologies to real-world challenges. We approach the field of biomanufacturing in a holistic manner, considering the optimization of the bioconversion process from different viewpoints including the microbial platform, the conditions within and their remote control, the biotransformation itself, and the implications beyond.
Research topics
- Developing genome engineering tools and strategies
- Increasing the robustness, performance and metabolic versatility of industrial microbial chassis
- Generating sustainable and safe-by-design products from alternative feedstocks and valorizable wastes
- Developing biosensing and modelling technologies for real-time data acquisition, processing and gathering actionable knowledge for the bioprocess
Expertise, techniques and infrastructure
- Synthetic biology: CRISPR technologies, oligonucleotide-mediated recombineering, genetic circuits, biosensors, combinatorial DNA assembly and genome engineering, high-throughput screening
- Metabolic engineering: new-to-nature metabolic configurations (e.g., C1-metabolism), growth-coupled scenarios, adaptive laboratory evolution (ALE), lifestyle engineering
- Bioproduction: using Pseudomonas putida as our main microbial chassis, but with research projects on Escherichia coli, Rhodobacter sphaeroides, Cutaneotrichosporon oleaginosus, Bacillus subtilis and Saccharomyces cerevisiae
- Metabolic modelling: model-driven design, Flux Balance Analysis (FBA)
- Digital Twins: DBTL, Design & Learn (DoE, ML), robotics, micro-fluidics, HTP Digital Twin technologies, semantic technologies
- Safety-and-Sustainability-by-Design: biosafety, valorisation, multi-stakeholder engagement
- Infrastructure: BIOTECH.NL, UNLOCK (Microbial communities), IBISBA (Industrial biotech & SynBio), ELIXIR & Data Science (Data, models, semantics)
Our projects
Microbial biosensor for environmental pollutants
Bacteria have developed ways to cope and survive in the ever-changing environment. With synthetic biology, we want to exploit these mechanisms and repurpose them to build microbial biosensor for environmental pollutants, such as PFAS, steroids, nitrates and phosphates, microcystins.
Thesis topics:
- Building chimeric proteins to sense steroids
- Design-build-test-learn approach to construct microbial biosensor for the forever chemical PFAS
- From lab bench to real-world: bridging the gap for synthetic biology applications
Contact persons: Sonia Mecacci, Enrique Asin Garcia
Microbial biosensor for environmental pollutants
Bacteria have developed ways to cope and survive in the ever-changing environment. With synthetic biology, we want to exploit these mechanisms and repurpose them to build microbial biosensor for environmental pollutants, such as PFAS, steroids, nitrates and phosphates, microcystins.
Thesis topics:
- Building chimeric proteins to sense steroids
- Design-build-test-learn approach to construct microbial biosensor for the forever chemical PFAS
- From lab bench to real-world: bridging the gap for synthetic biology applications
Contact persons: Sonia Mecacci, Enrique Asin Garcia
Engineering novel biosensor outputs
Bacteria have evolved sophisticated mechanisms to sense, respond to, and survive in changing environments. Synthetic biology enables us to repurpose these natural systems into microbial biosensors for environmental and biotechnological applications. This project focuses on engineering novel biosensor outputs. Possible thesis topics include:
- Engineering the production of new hyperspectral reporters in Pseudomonas putida / Saccharomyces cerevisiae for long-distance quantification of sensor activation
- CYBORG; protocol development for the generation of metabolically inactive microbial ‘cyborg’ cells.
- LOXmith; Generation of a modular, high-throughput, antibiotic-free genomic engineering platform in Pseudomonas putida
Contact persons: Nathan Haasbroek, Enrique Asin Garcia
Development and application of novel genome editing tools
To develop industry-ready microorganisms, strain engineering and synthetic biology nowadays require high-throughput approaches. Current microorganism genome editing tools struggle with generation of strains with stable genotype in a high-throughput, reliable manner, which makes strain development a time-consuming and expensive part of bioprocess design. The problem is further exacerbated when dealing with non-model microorganisms that are very different from well-studied and commonly used hosts.
This project aims to develop novel genome editing tools to address these shortcomings and to enable strain engineering in a wide range of microorganisms in a high-throughput, efficient, and iterative fashion. Upon development, the tools will be validated in industry-relevant showcases ranging from introducing alternative carbon-source metabolic pathways to optimizing pathways for aromatic molecule production.
Contact persons: Maxim Dronov, Enrique Asin Garcia
Contact us
Research themes
Bioprocess Engineering
Bioprocess Engineering, led by Rene Wijffels, teaches and develops innovative bio-based processes.
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