Metabolite studies in microbiome manufacturing

Just two phyla, Firmicutes and Bacteroidetes, represent 90% of the human gut microbiome; with the Clostridium genera representing 95% of the Firmicutes phyla, whereas Bacteroides and Prevotella dominate the Bacteroidetes phyla. Changes to the metabolite profile that occur over the course of a batch culture, upon alteration of polysaccharides in the media and upon scale up of microbial growths to ~5L for manufacturing processes are currently poorly understood. As such, Clostridium sp. will be the primary focus within this study, with growth and metabolite profile also examined in the presence of other bacteria (e.g. Bacteroides sp. And Prevotella sp.). This project will determine the metabolomic profile of an important microbial constituent of the microbiome, and seek to identify key metabolites and short-chain fatty acids that indicate the 'health' of a culture.

Key research questions: How do the metabolic profiles of Clostridium sp. cultures change in a 5 L microbial production fermenter system over time and in the presence of other bacteria such as Bacteroides sp. and Prevotella sp.? Can a fermenter system and control strategy be developed to maintain and manipulate the microbiome to generate beneficial products for use as therapeutics, medicinal compounds or raw materials (e.g. nutrients, synthetic biology)?

The student will combine the previous work done in the Horsfall group that provided a novel Clostridium sp. for investigation, and the Burgess lab, who developed a 5L microbial fermenter system directly linked to mass spec equipment for real time metabolomic analysis, to understand the metabolome within a representative microbiome culture at Edinburgh and Fujifilm.