High-throughput micro-fermentation for directed evolution and strain selection in industrial biotechnology

Scientific advances in industrial biotechnology (IB) and bio-based chemicals production have the potential to transform the global industrial landscape revolutionising sustainable manufacturing processes across all industrial sectors, including healthcare, sustainable energy, green chemistry, pharmaceuticals, novel materials and bioremediation. In fact, many of the challenges faced by industry and society (including energy demand and efficiency, replacement of fossil fuels and dealing with pollution, resource efficiency, food security, climate change and energy shortages) can now be tackled by bio-based production technologies. To exploit the potential of IB a thorough understanding of the performance of production strains and scale-up processes is critical.

The high-throughput bench top micro-fermentation system (Robolector-XL) provides a solution to a major challenge area of process/clone validation prior to extensive scale up studies. The RoboLector-XL (and other related systems) are now in extensive use by several industrial concerns and this has radically altered their approach to cell line development. This capability would provide a critical enabling technology to several areas of biotechnological research of focus within both the Manchester Institute of Biotechnology (MIB) and the wider University of Manchester (UoM) research environment, and will help drive the research towards exploitation and commercialisation.

One of the major hurdle in IB is that process conditions across different scales strongly effect the host cell productivity and such influence is non-linear across different candidate production clones. Whilst the reason for different parameters (mixing speeds, dissolved oxygen, temperature control), are well understood their influence is difficult to predict across different clones. This creates a scenario where the best clone at small scale (e.g. 96-well/shake-flask batch culture) is sub-optimal at large scale (e.g. 500L, fed-batch fermentation). Studying these parameters in parallel across a selection of clones would allow us to understand both which clones are likely to perform with optimal productivity at scale, but also and more importantly would allow us to understand the root cause(s) for the heterogeneous clone dependent response to different process conditions. Currently, we are lacking of an efficient micro-fermentation system that allows screening of multiple parallel cultures. The RoboLector-XL system allows micro-scale fermentation to be performed in parallel (48) with full process parameter monitoring and control (pH, dissolved oxygen (DO), growth rate, induction timing/rate). This system has online monitoring capability for the most commons fermentation parameters such as Cell Growth, pH, Dissolved Oxygen and fluorescent marker molecules, and can autonomously feed solutions, media, and inducers to each micro reactor according to a pre-defined timetable. The RoboLector-XL system provides a solution to a major challenge area of process/clone validation prior to extensive scale up studies and will enable large-scale clone screenings in different biotechnological areas.

The proposed parallel fermentation RoboLector-XL system platform will provide an important solution to the major challenge area of process/clone validation and enable thorough understanding of the performance of host cell production strains prior to scale up studies and inform exploitation of bio-based production technologies. The RoboLector-XL (and other related systems) is now in extensive use by several industrial concerns and has radically altered their approach to cell line development. This capability would provide a critical enabling technology to several areas of biotechnological research focus (e.g. screening and evaluation of industrially important yeast strains, biopharmaceutical protein production strains, CHO cell clones and bacterial production chassis) within both the Manchester Institute of Biotechnology (MIB) and the wider University of Manchester (UoM) research environment, and will help drive the research towards exploitation and commercialisation.

We will ensure close collaboration with our academic partners across the University and nationally in close partnership with other Synthetic Biology Research Centre's, DNA foundries and Universities, and reach out to industrial collaborators in the industrial biotechnology (IB), biomedicine and agri-food sectors. The equipment and associated training will provide a new capability for students and early career researchers in that will complement existing SynBio and IB capabilities. The resource will be overseen by senior experimental staff to ensure that it is well maintained, fit-for-purpose and remains accessible to academic and industrial researchers in the longer term. A user community (including external users) will be developed to facilitate the exchange of ideas and best practice and user protocols to maximize outputs. This will complement conventional methods of dissemination to the wider academic community through publication in peer-reviewed literature. We will work with networks and stakeholder/community groups to show-case applications and develop wider training.