The interplay between nutrient availability and secondary bile acid metabolism in commensal Clostridia mediates colonization resistance against C. difficile

共生梭状芽胞杆菌中营养可用性和次级胆汁酸代谢之间的相互作用介导对艰难梭菌的定植抵抗

• 批准号: 10622031
• 负责人: Casey Michelle Theriot
• 金额: $ 38万
• 依托单位: NORTH CAROLINA STATE UNIVERSITY RALEIGH
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-04-24 至 2028-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10622031
• 关键词: Affect; Amino Acids; Animal Model; Antibiotics; Area; Bacterial Physiology; Basic Science; Bile Acids; Biochemistry; Biological Process; Biomass; Clostridium difficile; Complex; Data; Development; Diet; Disease; Environment; Foundations; Germ-Free; Goals; Gram-Positive Bacteria; Growth; Health; Human; Immune response; In Vitro; Indigenous; Individual; Infection; Intelligence; Intestines; Knowledge; Laboratories; Mediating; Metabolism; Methods; Microbe; Mission; National Institute of General Medical Sciences; Nutrient; Nutrient availability; Prevention; Production; Protein Engineering; Proteins; Proteomics; Public Health; Reproducibility; Reproduction spores; Research; Role; Shapes; Structure; Techniques; Technology; Therapeutic; Therapeutic Intervention; United States National Institutes of Health; bacterial genetics; bile acid metabolism; colonization resistance; combinatorial; design; disease diagnosis; gut microbiome; gut microbiota; host-microbe interactions; improved; in vivo; metabolome; metabolomics; microbial; microbial community; microbiome; microbiome research; model organism; mouse model; novel; pathogen; prevent; therapeutic development; transcriptomics

Project Summary/Abstract In the Theriot laboratory we apply cutting-edge technology and high-throughput methods to analyze the gut microbiome and metabolome using a range of experimental techniques and animal models. We leverage many approaches that span diverse fields including bacterial genetics, bacterial physiology, protein engineering, biochemistry, and apply a variety of omic approaches (microbiomics, transcriptomics, proteomics, and metabolomics) in vitro and in vivo to define the mechanisms behind how the gut microbiota provides colonization resistance against C. difficile. One of the many essential functions of the indigenous gut microbiota is its ability to maintain colonization resistance and to prevent establishment and growth of pathogens in the gut. There has been a great deal of research in this area trying to define the mechanisms by which the gut microbiota mediates colonization resistance. Potential mechanisms include competition for nutrients, taking up physical space or biomass, production of inhibitory products, and shaping the host immune response. A popular model organism used to interrogate these mechanisms is Clostridioides difficile due to its exquisite sensitivity to changes in the gut microbiota structure and function. C. difficile is an anaerobic, spore-forming, Gram-positive bacterium first isolated in 1935 and the causative agent for C. difficile infection (CDI). Unlocking how C. difficile is able to benefit from the loss of colonization resistance in the gut has major implications for development of therapeutics for prevention and treatment of CDI. My long-term goal is to understand how the gut microbiota mediates colonization resistance against C. difficile. The overall objective of this application is to determine the relationship between nutrient availability (amino acids) and bile acid metabolism in the context of colonization resistance against C. difficile. Based on preliminary data our hypothesis is that amino acid availability influences secondary bile acid production by commensal Clostridia, which will alter colonization resistance against C. difficile. In order to investigate this hypothesis, we plan to alter amino acid abundances in defined and rich media in vitro, and use defined diets in vivo to understand how this impacts secondary bile acid production of commensal Clostridia. Leveraging our robust and reproducible germfree and antibiotic treated mouse models of CDI, we will determine how these metabolic processes affect the establishment and growth of C. difficile, as well as the surrounding gut microbial community. Using novel platforms like LC-IMS-MS and Protein-SIP, we will define the gut metabolome and metaproteome in the context of colonization resistance. The contribution of the proposed research is significant as it seeks to move away from untargeted therapies like FMT and move toward a targeted approach, whereby we can use diet (amino acids) to control secondary bile acid production by commensal Clostridia, restoring colonization resistance against C. difficile. The findings in this proposal will advance understanding of microbe-microbe interactions, host-microbe interactions, and improve microbiome-based therapeutics. Beyond C. difficile it has the potential to allow us to intelligently design customized therapeutic interventions to target human health conditions in the complex ecological environment of the human intestine.

项目概要/摘要 在 Theriot 实验室，我们应用尖端技术和高通量方法来分析肠道 使用一系列实验技术和动物模型来研究微生物组和代谢组。 我们利用许多 跨越不同领域的方法，包括细菌遗传学、细菌生理学、蛋白质工程、 生物化学，并应用各种组学方法（微生物组学、转录组学、蛋白质组学和 代谢组学）体外和体内以确定肠道微生物群如何提供背后的机制 针对艰难梭菌的定植抗性。 本土肠道微生物群的众多基本功能之一是其维持定植的能力 抵抗力并防止病原体在肠道内建立和生长。已经有很多 该领域的研究试图确定肠道微生物群介导定植的机制 反抗。潜在的机制包括争夺营养物质、占用物理空间或生物量、 抑制产品的生产，并塑造宿主免疫反应。一种流行的模式生物用于 质疑这些机制的是艰难梭菌，因为它对肠道变化非常敏感 微生物群的结构和功能。艰难梭菌首先是一种厌氧、产芽孢、革兰氏阳性细菌 1935 年分离出来，是艰难梭菌感染 (CDI) 的病原体。解锁艰难梭菌如何能够 肠道内定植抗性丧失的益处对以下疾病的发展具有重大影响： 预防和治疗 CDI 的疗法。 我的长期目标是了解肠道微生物群如何介导针对艰难梭菌的定植抵抗力。 该应用程序的总体目标是确定营养物质可用性（氨基）之间的关系 酸）和胆汁酸代谢在针对艰难梭菌定植抗性的背景下。基于 初步数据我们的假设是氨基酸的可用性通过以下方式影响次级胆汁酸的产生 共生梭菌，这将改变对艰难梭菌的定植抵抗力。为了调查此事 假设，我们计划在体外改变限定培养基和丰富培养基中的氨基酸丰度，并在 体内了解这如何影响共生梭菌的次级胆汁酸产生。利用我们的 稳健且可重复的无菌和抗生素治疗的 CDI 小鼠模型，我们将确定这些模型如何 代谢过程影响艰难梭菌以及周围肠道微生物的建立和生长 社区。使用 LC-IMS-MS 和 Protein-SIP 等新颖平台，我们将定义肠道代谢组并 定植抗性背景下的宏蛋白质组。 拟议研究的贡献是重大的，因为它试图摆脱非靶向治疗 像 FMT 一样，朝着有针对性的方法迈进，我们可以使用饮食（氨基酸）来控制继发性 共生梭菌产生胆汁酸，恢复对艰难梭菌的定植抵抗力。研究结果 该提案将增进对微生物-微生物相互作用、宿主-微生物相互作用以及 改善基于微生物组的疗法。除了艰难梭菌之外，它还有可能让我们智能地 设计定制的治疗干预措施以针对复杂生态环境中的人类健康状况 人体肠道环境。