Synthetic biology of methane oxidising bacteria for the production of high-quality feed protein

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BACKGROUND: Healthy poultry require high quality sources of protein and carbohydrates. Modern feeds for poultry consists largely of grain and protein sources such as soybean, which can be in direct competition with human food consumption. Countries like Canada and US have recently been active in producing high protein insects for animal feeds (Enterra Feed Corporation), and received national regulatory approval for use in broiler feed and pet food, the first ingredient of its kind to do so. Similarly, the EU recently (August 2021) approved the use of processed insect protein in poultry and pig feed. To meet poultry feed market demand in a way that tackles both environmental and economic concerns, we propose a novel route to poultry feed using methane (CH4) fixing bacteria, methanotrophs. These bacteria have a proven commercial track record for single cell protein production (for fish feed), as well as naturally producing lipids. Methanotrophs also utilize methane as the sole source of carbon and energy, providing significant advantages in both process economics and sustainability. Methane (CH4) is an abundant and cheap carbon resource, but is currently under-utilised as a feedstock for industrial biotechnology and is more associated as a greenhouse gas (GHG) pollutant. Methane is also a major component of biogas produced on a large scale by anaerobic digestion, technology that is well established in the UK. Today, most biogenic methane is burnt for energy and has relatively little value. Being a low-cost and sustainable feedstock, given the many sources available and current wastage and associated GHG ramifications, methane provides an exciting feedstock opportunity for fermentation and conversion into high value biochemical metabolites (lipids, proteins and feeds). As the world-leading methane-based protein producer, Calysta has demonstrated the use of methanotrophs in the commercial-scale production of nutritional ingredients and feed from methane. Methylococcus capsulatus is their process organism, which has already been approved in the EU for feeding to farmed fish and livestock such as pigs. Methane fermentations on a large scale would reduce the demand for land to grow food for livestock. However, more research is needed on methanotroph-based poultry feed and the workhorse of the process, methane-fixing bacteria. AIM: In this project, we will explore the suitability of methane-fixing bacteria in the form of single cell protein as a potential high quality protein source in chicken feed. STRATEGY: Our group recently established an arsenal of genetic tools in M. capsulatus, including CRISPR/Cas9, CRISPRi, Tn5 transposon, which will allow us to investigate and enhance the methane fixation rate in M. capsulatus and manipulate the biomass composition of bacteria to enhance their functionality as an ingredient of chicken feed.The main project tasks will be: (i) identify Tn5 transposon mutants with modified biomass composition and/or growth profile, investigate the gene and/or pathway involved in the modification using our newly developed CRISPR technology; (ii) characterize chosen mutants for its performance in lab scale gas fermentation bioreactors, using the wildtype and a glycogen minus M. capsulatus strains as benchmarks; (iii) investigate the inactive Calvin-Benson-Bassham cycle in M. capsulatus using a combined approach of system and synthetic biology; (v) carry out a small scale feed test on broiler chickens using feed made from a chosen improved M. capsulatus, to determine its potential as an alternative and novel source of protein in chicken feed formulation. OUTCOME: Working with one of the world's leading C1 companies, the student will develop and demonstrate the potential of M. capsulatus as whole cell protein feed from low cost methane gas. This will allow avoidance of competition with food and land resources while providing benefits to the environment and society through reduction in GHG emiss