Climate change, pollution and depletion of reserves drive the search for alternatives to fossil-based resources. Micro-organisms capable of converting sustainable resources into valuable compounds (microbial cell factories, MCFs) can replace (petro)chemical products and processes, and are critical in the transition to a sustainable society. However, widespread industrial implementation of MCFs is hampered by inefficiency, instability, and complexity of current bioprocesses. Therefore INDUSTRIOPHILE develops a systematic approach to discover and improve traits in MCFs, to make them tolerant to industrial conditionals and capable of efficient production of a broad range of products. The INDUSTROPHILE approach is validated through four industrial showcases.

Microorganisms can be modified to sustainably produce a variety of natural products such as aromas or vitamins. Engineering these microbial cell factories is not an easy task and computational models and machine learning methods can help us in this endeavour. We have experimentally generated data that has been used to train computational and machine learning models. These models have suggested new improved designs we are currently testing. Thus we are improving our microorganism and we are also developing methods to efficiently and rapidly generate adequate cell factories that will allow the transition to a bio-based economy.

The UNLOCK facility provides a unique platform for breakthroughs in knowledge and application of mixed microbial cultures, thereby providing the means to solve some of the major societal challenges facing food safety and production, human, animal and environmental health, bio-resource utilization and sustainable production of plug-in commodity chemicals by the biotech industry. Research methods for investigation of microbial communities and their interaction with the environment develop very fast due to novel advanced molecular tools that need to be integrated with more traditional cultivation based methods. Effective dealing with the increased complexity of these experimental procedures requires a standardized research infrastructure as defined in UNLOCK. One of the major challenges defined in UNLOCK is the integration and optimization of the hard- and software side of the infrastructure. The most important threat for development of the UNLOCK platform is that the hard- and software integration, standardization, and optimization elaborated in the development phase of UNLOCK cannot be established. Also, the currently available momentum driven by the expressed expectations and needs of potential academic and industrial users would be lost at least to an important extent. The bridge funding proposed here will be distributed among three tasks, associated with the different complementary expertise of the partners involved in UNLOCK. The three core activities of UNLOCK are covered in this bridge funding proposal: (i) microbial culture cultivation and functional characterization, (ii) molecular community characterization using molecular methods, and (iii) data handling, processing & interpretation.

For professionals in life sciences and health (LSH), its increasingly crucial to (i) efficiently link findable, accessible, interoperable, and reusable (FAIR) data with computational workflows that process the data (FAIR workflows); (ii) ensure that the data produced by FAIR workflows can be seamlessly utilized for artificial intelligence (AI) applications (AI-ready); (iii) construct AI models while integrating pertinent domain-specific knowledge (AI-savvy). The objective of this project is to create two new post-Master’s courses on FAIR workflows and advanced machine learning/modern AI technology for life sciences. These courses aim to address the existing gap in equipping researchers with these essential skills.

Microorganisms can perform many processes useful for mankind, such as converting milk to cheese, keeping human and animal intestines healthy, and cleaning our water and environment. So far, we are relying heavily on pure cultures, and only exploited less than 1% of the microorganisms present in nature. In Wageningen and Delft the UNLOCK research facility is built enabling the discovery, characterization, optimization and utilization of microbial functionalities in natural and man-made microbial ecosystems to solve some of the major societal challenges facing food safety and production, human, animal and environmental health, and bioresource utilization and sustainable production of biobased chemicals.