Stochasticity-resilient control of microbial communities in bioprocessing

Cooperation and competition between microbial species that share the same environment drive niche-specialisation and higher-level community organisation. In contrast to natural microbial communities, which have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia, synthetic microbial communities are well-defined and have reduced complexity. Engineered communities are increasingly finding their way into diverse biotechnological applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. Microbial biotechnology benefits from consortia due to the unique catalytic activities of each member, their ability to use complex substrates, compartmentalization of pathways, and distribution of molecular burden. Furthermore, the construction of the microbial consortia is enhanced by computational models through the prediction of preferred metabolic cross-feeding networks and inference on population dynamics over time.

Recent work on perturbations on microbiomes demonstrated that many dynamic transitions follow stochastic rather than deterministic paths, and therefore result in shifts to/from unstable and highly variable community states. The term the 'Anna Karenina principle' was coined to describe this argument, based on the quote from Leo Tolstoy that "all happy families look alike; each unhappy family is unhappy in its own way." This notion highlights a major obstacle in the successful utilisation of microbial communitites in well-controlled bioprocess settings.

This project aims to address the above stated challenge by discovering metabolic identifiers that withstand the stochastic variations in synthetic community structures, which will allow robust and tuneable control in a bioprocess setting. Community metabolic networks will first be investigated by stochastic metabolic modelling; the candidate metabolic markers identified by modelling will then be used to design a platform for monitoring metabolic markers during growth. The high-throughput platform will allow sufficient variability in community structures to monitor the response to stochasticity. Promising named markers will then be used to implement control actions for a benchtop fermentation process that is designed for the synthetic community. The analyses will be carried out on synthetic (i) mixed bacterial and yeast communities of suspended cells, and (ii) mixed bacterial communities of immobilised cells in biofilms. The analysis of different community structures will inform on the generalisability of the findings.

Our goal is to harness the RhoGTPase signalling pathway to create a shape-shifting living tissue that can be controlled by light, inspired by the design rules observed during embryonic morphogenesis. We will focus on two aims. First, we will design molecular actuators controlling cell mechanics based on optogenetics with one actuator increasing contractility (based on a RhoGEF) and the other decreasing contractility (based on a RhoGAP). We will then characterise their effects on cell and tissue mechanics at minute to hour time-scales. In the second aim, we will integrate these data into a computational framework that combines the theory of elasticity for tissues and evolutionary algorithms. The computational framework will suggest spatiotemporal actuation patterns to reach any desired tissue shape and we will implement these in experiments. We will focus in particular on synthetically replicating morphogenetic changes observed during embryonic development.

The 2016 UK Roadmap Bio-design for the Bio-economy highlighted the substantial impact that synthetic biology can bring to the UK and global economies by developing: frontier science and technology; establishing a healthy innovation pipeline; a highly skilled workforce and an environment in which innovative science and businesses can thrive. Synthetic biology promises to transform the UK Bio-economy landscape, bringing bio-sustainable and affordable manufacturing routes to all industrial sectors and will ensure society can tackle many contemporary global Grand Challenges including: Sustainable Manufacturing, Environmental Sustainability Energy, Global Healthcare, and Urban Development. Whilst synthetic biology is burgeoning in the UK, we now need to build on the investments made and take a further lead in training next generation scientists to ensure sustained growth of a capable workforce to underpin the science base development and growth in an advanced UK bio-economy.
This training provided by this CDT will give students from diverse backgrounds a unique synthesis of computational, biomolecular and cellular engineering skills, a peer-to-peer and industrial network, and unique entrepreneurial insight. In so doing, it will address key EPSRC priority areas and Bioeconomy strategic priorities including: Next-generation therapeutics; Engineered biomaterials; Renewable alternatives for fuels, chemicals and other small molecules; Reliable, predictable, and scalable bioprocesses; Sustainable future; Lifelong health & wellbeing.
Advances created by our BioDesign Engineering approach will address major societal challenges by delivering new routes for chemical/pharma/materials manufacture through to sustainable energy, whilst providing clean growth and reductions in energy use, greenhouse gas emissions and carbon footprints. Increased industry awareness of bio-options with better civic understanding will drive end-user demand to create market pull for products. The CDT benefits from unrivalled existing academic-industry frameworks at the host institutions, which will provide direct links to industrial partners and a direct pathway to early economic and industrial impact.

This CDT will develop 80-100 next-generation scientists and technologists (via the funded cohort and wider integration of aligned students at the three institutions) as adept scientists and engineers, instilled with technical leadership, who as broadly trained individuals will fill key skills gaps and could be expected to impact internationally through leadership roles in the medium term. Importantly the CDT addresses key skill-gaps identified with industry, which are urgently required to create and support high value jobs that will enable the UK to compete in global markets. Commercialisation and entrepreneurship training will equip the next generation of visionaries and leaders needed to accelerate and support the creation of new innovative companies to exploit these new technologies and opportunities.

The UK government identified Synthetic Biology as one of the "Eight Great Technologies" that could be a key enabler to economic and societal development. This CDT will be at the forefront of research that will accelerate the clean growth agenda and the development of a resilient circular bioeconomy, and will align with key EPSRC prosperity outcomes including a productive, healthy and resilient nation. To foster wider societal impact, the CDT will expect all students to contribute to public outreach and engagement activities including: open days, schools visits, and science festival events: students will participate in an outreach programme, with special focus on widening participation.

This CDT will contribute to the development of industrial strategy through the Synthetic Biology Leadership Council (SBLC), Industrial Biotechnology Leadership Forum (IBLF), and wider Networks in Industrial Biotechnology and Bioenergy and Professional Institutes.