Engineering synthetic microbial consortia for next-generation biotechnology

Natural ecosystems are composed of cohorts of microorganisms where the ensemble genetic biodiversity allows efficient utilisation of habitat resources. In contrast, industrial bioprocessing applications currently employ microbial cultures inoculated with a single microbial species, which limits processing of raw materials and end products to the properties conferred by the genetic material of one particular species. With the advent of Synthetic Biology and the availability of low-cost chemical synthesis of DNA, synthetic microbial consortia can be designed with engineered microbial species to capture the beneficial properties of genetic diversity and division of labour in a similar way to what is happening in nature.

In this project, we aim to build the tools necessary for the rational design of synthetic microbial consortia for use in industrial bioprocess applications. As part of an integrated design process, we will extract cell-cell communication systems found in nature. In particular, we will use bioinformatics tools to "mine" such systems from publicly available sequence databases with a novel approach for the identification of systems that exhibit no/minimal signal cross-talk. We will then use synthetic biology technologies to produce cell-to-cell communication devices from the bioinformatics data. High-throughput, fluorescence-based gene expression assays will be used for the assessment of functionality. Once the communication devices are established, we will identify metabolic pathways that are susceptible to benefit from a division of labour. Such pathways will be transferred using advanced DNA assembly methods and novel CRISPR tools to maximise the bioproduction of high-value molecules such as fuels, chemicals or nutraceuticals.

The ability to rationally design microbial consortia for industrial bioprocessing applications can aid efforts for a more sustainable future. This can be achieved through the use of bio-based processes in the manufacturing of chemicals and other molecules where synthetic microbial consortia rich in genetic content will allow the re-cycling of raw resources such as wastes back into the productive processes of society rather than environmentally harmful disposal alternatives such as incineration or burying in landfills.

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.