Towards biofilm reactors for flow biocatalysis: investigating the productivity of biofilms for commodity chemical production in a microfluidic scale-d

Title: Towards biofilm reactors for flow biocatalysis: investigating the productivity of biofilms for commodity chemical production in a microfluidic scale-down model

Supervisors and affiliations
Professor Nicolas Szita, University College London
Professor Gary Lye, University College London

Collaborating academics at UCL Dept Biochemical Engineering
Professor John Ward, Dr Marco Marques, Dr Duygu Dikicioglu,
Collaborating academics outside UCL
Prof Nigel Scrutton, University of Manchester

Context
The field of continuous flow synthesis has grown significantly over the last two decades. Whilst the application of continuous flow focussed more on chemical synthesis initially, recently the use of whole cells and enzymes for biocatalytic synthesis has become popular. The use continuous flow for biocatalytic synthesis is termed 'Flow Biocatalysis'. Continuous flow allows the biocatalytic process to be performed in a heterogeneous catalysis regime. More importantly, flow biocatalysis reactors offer improved mass and heat transfer, automation (reducing process variations), in-line purification and pressurised operation. And the flow systems can be integrated with process analytical technology (PAT). Flow Biocatalysis therefore enables the establishment of new process windows for the synthesis of pharmaceuticals, value-added chemicals, and materials.

Aims and Objectives
In this PhD project, we will evaluate and further explore the use of biofilms specifically for their application in flow biocatalysis (whole-cell biocatalysis) and flow biocatalysis reactors for commodity chemicals production.
The first hypothesis to test is thus whether a microfluidic culture device can be employed for forming and maintaining biofilms in the device. Evaluating how well the biofilm and the bacterial culture can be retained in (or limited to) the culture chamber area will be of particular interest (given the continuous, perfusion mode of the device).
The second hypothesis is that conditions can be found where the cells in a biofilm outperform non-biofilm growing cells. Related to that, as a sub-hypothesis, that biofilm-based systems outperform enzyme-based systems. Metrics for comparison include productivity of citramalate per cell mass (enzyme protein mass), yield of citramalate on substrate, and space time yield where possible (reactor configuration), for different dilution rates, i.e. different levels of hydrodynamic shear stresses.

Research Methodology
Conditions to investigate will include single biofilm growing bacteria vs co-culture, concentration of carbon source (potentially different types), cell growth substrate, hydrodynamic shear stress (in high shear environments, biofilms may be flatter or form long strands), and physico-chemical conditions, such as hydrodynamic shear stress and dissolved oxygen levels. By analysing the productivity per cell, we will determine optimal conditions for the biofilms.
The knowledge gained from this research is expected to provide design criteria for flow biocatalysis reactors, such as the structural/scaffold support to maintain optimal metabolite producing conditions at different scales. Of interest could be biofilm-immobilisation structures, such as surface-immobilised biofilms, monoliths to scaffold biofilms, and porous/hydrogel-like beads which may foster particular spatial arrangements for the biofilm.

Alignment to EPSRC's strategies and research areas
The project aligns with Future Manufacturing Technologies

The CDT has a proven track record of delivering impact from its research and training activities and this will continue in the new Centre. The main types of impact relate to: (i) provision of highly skilled EngD and sPhD graduates; (ii) generation of intellectual property (IP) in support of collaborating companies or for spin-out company creation; (iii) knowledge exchange to the wider bioprocess-using industries; (iv) benefits to patients in terms of new and more cost effective medicines, and (v) benefits to the wider society via involvement in public engagement activities and impacts on policy.

With regard to training, provision of future bioindustry leaders is the primary output of the CDT and some 96% of previous EngD graduates have progressed to relevant bioindustry careers. These highly skilled individuals help catalyse private sector innovation and biomanufacturing activity. This is of enormous importance to capitalise on emerging markets, such as Advanced Therapy Medicinal Products (ATMPs), and to create new jobs and a skilled labour force to underpin economic growth. The CDT will deliver new, flexible on-line training modules on complex biological products manufacture that will be made available to the wider bioprocessing community. It will also provide researchers with opportunities for international company placements and cross-cohort training between UCL and SSPC via a new annual Summer School and Conference.

In terms of IP generation, each industry-collaborative EngD project will have direct impact on the industry sponsor in terms of new technology generation and improvements to existing processes or procedures. Where substantial IP is generated in EngD or sPhD programmes, this has the potential to lead to spin-out company creation and job creation with wider economic benefit. CDT research has already led to creation of a number of successful spin-out companies and licensing agreements. Once arising IP is protected the existing UCL and NIBRT post-experience training programmes provide opportunities for wider industrial dissemination and impact of CDT research and training materials.

CDT projects will address production of new ATMPs or improvements to the manufacture of the next generation of complex biological products that will directly benefit healthcare providers and patients. Examples arising from previous EngD projects have included engineered enzymes for greener pharmaceutical synthesis, novel bioprocess operations to reduce biopharmaceutical manufacturing costs and the translation of early stem cell therapies into clinical trials. In each case the individual researchers have been important champions of knowledge exchange to their collaborating companies.

Finally, in terms of wider public engagement and society, the CDT has achieved substantial impact via involvement of staff and researchers in activities with schools (e.g. STEMnet), presentations at science fairs (Big Bang, Cheltenham), delivery of high profile public lectures (Wellcome Trust, Royal Institution) as well as TV and radio presentations. The next generation of CDT researchers will receive new training on the principles of Responsible Innovation (RI) that will be embedded in their research and help inform their public engagement activities and impact on policy.