Metabolite studies in microbiome manufacturing

只有两个门，厚壁菌门和拟杆菌门，占人类肠道微生物组的90%;梭菌属占厚壁菌门的95%，而拟杆菌和普雷沃菌占拟杆菌门的主导地位。目前对分批培养过程中、培养基中多糖改变后以及生产工艺中微生物生长规模扩大至约5 L时发生的代谢产物谱变化知之甚少。因此，梭菌属将是本研究的主要关注点，在存在其他细菌（例如拟杆菌属和普雷沃菌属）的情况下也检查了生长和代谢产物谱。该项目将确定微生物组的重要微生物成分的代谢组学特征，并寻求确定表明培养物“健康”的关键代谢物和短链脂肪酸。关键研究问题：在5 L微生物生产发酵罐系统中，在存在其他细菌（如拟杆菌属和普雷沃氏菌属）的情况下，梭菌属培养物的代谢谱如何随时间发生变化？是否可以开发发酵罐系统和控制策略来维持和操纵微生物组，以产生有益的产品，用作治疗剂，药用化合物或原材料（例如营养素，合成生物学）？学生将联合收割机在Horsfall组，提供了一种新的梭菌属以前所做的工作。调查，和伯吉斯实验室，谁开发了一个5升微生物发酵罐系统直接连接到质谱设备真实的时间代谢组学分析，了解代谢组内的代表性微生物组培养在爱丁堡和富士胶片。

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.