Engineering Biology

We engineer microbes to make useful products from greenhouse gases, waste products and low-cost feedstocks. Our work has the potential to make clean, sustainable and affordable products including transport fuels, useful chemicals, animal feed, vaccines and pharmaceuticals, and in turn reduce societal reliance on fossil fuels. Our ambition is to develop the technologies required to implement a more sustainable bioeconomy.

Engineering Biology research in the Biodiscovery Institute includes the BBSRC/EPSRC Synthetic Biology Research Centre (SBRC) and the Nottingham Engineering Biology Labs (NEBL).

SBRC Nottingham

The SBRC is a world-leading centre for Clostridium research and microbial gas-fermentation. It has a multidisciplinary critical mass of around 100 researchers funded by research councils and industry. The SBRC works with a range of microbes capable of recycling carbon into the chemicals and fuels modern society needs in a sustainable manner. These include aerobes and anaerobes, mesophiles and thermophiles, as well as saccharolytic, proteolytic and autotrophic chassis. Synthetic biology approaches using metabolic engineering, proprietary genome engineering tools and systems approaches are being used to optimise each chassis for the conversion of waste gases and biomass into industrially useful fuels and chemicals.

The SBRC is also involved in therapeutic biotechnology including genetically engineer Clostridium botulinum to study its physiology and to engineer safe strains. Allied to this work are studies aimed at the development of countermeasures against Clostridioides difficile infection, including vaccine development, phage therapy and preventing spore germination in the microbiota. Through re-wiring of the clostridial sporulation pathway, a suite of strains are in development that will be used in tumour and microbiome delivery and in large scale, fermentation-based manufacturing processes.

An independent external review of the SBRC facilities stated that they were "the most comprehensive facilities in microbial gas fermentation seen anywhere in the world". The SBRC occupies an entire floor of the Biodiscovery Institute’s research facility and has bespoke robotics platforms, 11 double anaerobic microbiological cabinets, two suites of LC, LC-MS, GC and GC-MS analytics and three suites of microbial gas fermentation facilities enabling parallel fermentation at lab-scale as batch or continuous culture in both aerobic and anaerobic conditions.

Nottingham Engineering Biology Labs (NEBL)

NEBL use a range of genetic and biological techniques to engineer microbes with new useful properties. We develop powerful synthetic biology technologies including massively parallel genetic design and construction, and design or edit DNA from individual DNA bases (‘letters’) all the way up to rewriting whole genomes. We apply these technologies to engineering microbes and their metabolism for applications in biomanufacturing, biocatalysis, sustainability, and health; often using diverse organisms best suited to each challenge, including Clostridium, E. coli, yeast and cyanobacteria.

Research highlights

The SBRC-Nottingham researches both aerobic and anaerobic microbial systems but its primary focus is aerobic gas fermentation utilising Cupriavidus necator to make: 1,3 butanediol, mevalonate, isoprene, 3-hydroxyproprionate, isopropanol, acetone and 2,3 butanediol with the aim of optimising production to make all of these molecules from greenhouse gases and hydrogen. In addition, we are harnessing the potential of the Clostridium species in several applications including from cancer treatment to solvent production. Most of our work is funded through the EPSRC and BBSRC and we are particularly active in working with industry and supporting new spin-out enterprises.

Nottingham Engineering Biology Labs (NEBL) research highlights include:

• ‘Start-Stop Assembly’, an improved technology for DNA assembly, optimised for metabolic engineering and for transfer to diverse organisms
• Development and application of synthetic DNA ‘parts’ for building genetic systems in Clostridium and cyanobacteria
• Improving external control of gene expression in E. coli and cyanobacteria
• Development of a high-throughput system for laboratory evolution and its application to evolve useful new variants of several industrially-relevant types of enzymes
• Construction and debugging of yeast synthetic chromosomes, including new chromosomes allowing genome size reduction
• Use of the SCRaMbLE recombinase system encoded into the yeast synthetic genome to optimise yeast for pharmaceutical production, new substrate utilisation and environmental stress resistance
• Developing synthetic genomics techniques using yeast as a chromosome-scale DNA assembly platform

Find out more about SBRC research

Find out more about NEBL research

Our researchers

Search the table below to find out more about our researchers. You are able to filter the table by searching for names, keywords, and techniques.

 

Full list of our researchers

Name	Research keywords	Research techniques
Ben Blount	Synthetic genomics, synthetic biology, microbial strain engineering, genome engineering, yeast genetics	DNA assembly, CRISPR, chromosome design, SCRaMbLE
Daniel Booth	Chromosomes, mitosis, advanced-imaging, cancer, cell-division	CLEM, electron microscopy, advanced proteomics, advanced imaging, light microscopy, volume microscopy
Lee Buttery	3D cell models, stem cells, osteoblasts, cell-materials interactions, tissue engineering	3D and ES cell culture, osteoblast culture, immunocytochemistry, optical tweezers for cell biology
Miguel Camara	Biofilms, quorum sensing, antimicrobials, microbial gene regulation, antimicrobial target discovery	Biofilm model design, biofilm imaging, bacterial transcriptomics, bioreporter design, HTP antimicrobial testing
Ingrid Dreveny	Proteases in the ubiquitin system, protein structure, structure-aided drug design, enzyme specificity, proteins in biotechnology	Macromolecular X-ray crystallography, isothermal titration calorimetry, biochemistry, protein engineering
Ruth Griffin	Oral vaccine delivery systems, infectious diseases	Gene cloning and protein purification, formulation, in vivo immunogenicity and challenge studies, antibody assays
John Heap	Engineering biology/ synthetic biology, metabolic engineering, biotechnology, biocatalysis, enzyme evolution	Engineering biology/ synthetic biology, metabolic engineering, biotechnology, biocatalysis, enzyme evolution
Stephan Heeb	Bacterial infections, virulence, quorum sensing, gene expression, antimicrobial strategies	Bacterial genomics, RNA-Seq, RNA-protein interactions, construction of bacterial vectors
Katalin Kovacs	Engineering biology, metabolic engineering, autotrophic microorganisms, bioelectochemical synthesis, circular economy	Molecular biology, microscopy, microbial cultivation, electrofermentation, plastid engineering
Alvaro Mata	Biomaterials, tissue engineering, regenerative materials, in vitro models, biomineralization	Self-assembly, bioprinting, electron microscopy
Nigel Minton	Exploiting autotrophy, reducing carbon emissions, industrial biotechnology, microbial pathogenesis, anaerobes	Synthetic biology, metabolic engineering, gas fermentation, genome editing, therapeutic delivery systems
Paloma Ordóñez Morán	Stem cells, inflammation, differentiation, cancer, tumour heterogeneity	3D organoids, primary mouse and human cell culture, stem cell-based approaches, in vivo assays, gene expression
Ellis O'Neil	Natural products, algal biotechnology, biotransformation	Analytical chemistry, mass spectrometry, protein expression and purification, genome mining
Philippe Soucaille	Metabolic engineering, systems biology, synthetic biology, microbial physiology – CO2 fixation	Enzyme evolution, bacterial genome editing, fluxomics, proteomics, transcriptomics
Neil Thomas	Enzyme mechanism, enzyme inhibitors, biopharmaceutics, silk and other protein-based biomaterials, nanobiotechnology	Bioconjugation, chemiluminescence, un-natural amino acid mutagenesis, enzyme activity assays, enzyme inhibitor design
Huw Williams	NMR, molecular interactions, molecular structure, analytical, kinetics	NMR, molecular interactions, solid state NMR, molecular dynamics, molecular structure
Klaus Winzer	Microbial metabolism, biological engineering, synthetic biology, bacterial carbon capture, quorum sensing	Anaerobic microbiology, gas fermentation, genetic modification of bacteria, adaptive laboratory evolution
Jing Yang	Biomaterials, 3D bioprinting, tissue engineering, regenerative medicine, immunomodulatory materials	3D printing, biomaterial preparation, chemical characterisation, mechanical testing, cell culture
Mischa Zelzer	Biointerfaces; biomaterials; peptide materials; hydrogels; computational material science	Surface modification and analysis; polymerisation kinetics; light and enzyme responsive materials; material characterisation
Ying Zhang	Industrial biotechnology, biological engineering, single-carbon utilising bacteria for carbon capture, sustainable bioproducts, biorecovery.	Synthetic biology, bacterial genome editing, metabolic engineering, protein engineering, strain improvement

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