Gnotobiotics mice and bacterial cultures phenotyping core

知生小鼠和细菌培养表型核心

• 批准号: 10241903
• 负责人: Eric C Martens
• 金额: $ 21.55万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10241903
• 关键词: 16S ribosomal RNA sequencing; Activities of Daily Living; Address; Anaerobic Bacteria; Automobile Driving; Bacterial Genome; Behavior; Bile Acids; Biological Assay; Biological Models; Butyrates; Carbohydrates; Communities; Complex; Consumption; Coupled; Custom; Development; Diet; Disease; Disease Progression; Disease model; Ecosystem; Enterococcus; Enterococcus faecalis; Fiber; Foundations; Gastrointestinal tract structure; Generations; Genes; Genetic; Genome; Gnotobiotic; Goals; Growth; Human; Hydrolase; Hydrolysis; Implant; In Vitro; Individual; Infection; Intervention; Knowledge; Martens; Measurement; Measures; Metabolic; Metabolism; Metagenomics; Microbe; Modeling; Modification; Mucous Membrane; Mus; Nutrient; Organism; Outcome; Patients; Phenotype; Polysaccharides; Positioning Attribute; Potato; Production; Refractory; Renaissance; Resistance; Resources; Role; Sampling; Starch; Symbiosis; System; Technology; Testing; Time; Transplantation; Variant; Work; bile salts; dietary; experience; experimental study; fecal transplantation; genome sequencing; graft vs host disease; gut bacteria; gut microbes; gut microbiome; host microbiome; individual patient; insight; lens; member; metabolic phenotype; metagenome; microbial; microbial community; microbial composition; microbiome research; microbiota; microorganism; microorganism interaction; preservation; reconstitution; response; symbiont; synthetic construct

PROJECT SUMMARY/ABSTRACT – CORE C A major need in host-microbiome research is the development of tractable model systems that provide a path to understand the mechanistic contributions of gut microbes to various diseases in which they participate. Germfree mice implanted with “synthetic communities” of cultured microorganisms, provide such a path as the resulting “gnotobiotic mouse” only contains microbes of known identity and often genome sequence. However, even when cultured and fully sequenced microbes are used, a major limitation is understanding the metabolic potential of the microbes involved. High-throughput metabolic phenotyping of cultured microbes helps to address the knowledge gap associated with the latter point. The main goals of the Microbial Phenotyping and Gnotobiotic Model Core will be to 1. Provide the resources for culturing and combining existing microbes associated with resistant starch degradation, butyrate production, H2 consumption and bile salt hydrolysis; 2. Perform targeted and deep culture on patient samples that vary in their responses to resistant starch consumption with the goal of modeling these variations in gnotobiotic mice colonized with the isolated species; and 3. Perform metabolic phenotyping combined with genome sequencing on isolated microbes so that their causal roles in determining the outcomes of resistant starch consumption on GVHD and bile acid modification on Enterococcus infection can be investigated through the lens of defined functions. In the latter case, such functions will include phenotypes believed to be directly involved the outcomes of the proposed disease models (degradation of resistant starch, butyrate production and bile salt hydrolases activity). However, we also anticipate extending our phenotypic measurements to define other metabolic facets, such as microbial interactions with dietary nutrients beyond resistant starch, so that we can better understand their contributions to community behavior, butyrate production, etc. The Martens Lab has extensive experience assaying cultured human gut bacteria in custom phenotypic growth arrays (e.g., for broadly measuring polysaccharide-degrading abilities), building synthetic communities from groups of microbes with defined phenotypes and driving differences in host disease progression through exogenous forces on the microbiota, such as diet. This core will be foundational to the execution of experiments in several of the proposed projects and will also establish the resources for building complex gnotobiotic systems that still preserve an experimental path towards defining mechanisms.

项目概要/摘要 – 核心 C 宿主微生物组研究的一个主要需求是开发易于处理的模型系统，该系统提供 了解肠道微生物对各种疾病的机制贡献的途径 植入培养微生物“合成群落”的无菌小鼠，提供。 这样的路径是由此产生的“无菌小鼠”仅包含已知身份的微生物，并且通常 然而，即使使用培养和完全测序的微生物，一个主要的因素仍然存在。 限制是了解所涉及微生物的代谢潜力。 培养微生物的表型分析有助于解决与后一点相关的知识差距。 微生物表型和知生模型核心的主要目标是 1. 提供 用于培养和组合与抗性淀粉降解相关的现有微生物的资源， 丁酸盐产生、H2消耗和胆汁盐水解；2.进行定向深度培养； 患者样本对抗性淀粉消耗的反应各不相同，目的是建模 3. 进行代谢； 表型分析与分离微生物的基因组测序相结合，以便了解它们在 确定抗性淀粉消耗对 GVHD 的影响以及胆汁酸修饰对 GVHD 的影响 在后一种情况下，可以通过定义功能的透镜来研究肠球菌感染。 这些功能将包括被认为直接涉及拟议结果的表型 疾病模型（抗性淀粉降解、丁酸盐产生和胆汁盐水解酶活性）。 然而，我们还预计将我们的表型测量扩展到定义其他代谢方面， 例如微生物与抗性淀粉以外的膳食营养素的相互作用，以便我们能够更好地 了解他们对社区行为、丁酸盐生产等的贡献。Martens 实验室 在定制表型生长阵列中分析培养的人类肠道细菌的丰富经验（例如， 用于广泛测量多糖降解能力），从群体中构建合成群落 具有明确表型的微生物并通过驱动宿主疾病进展的差异 对微生物群的外源力量，例如饮食，将是执行的基础。 在几个拟议项目中进行实验，并将建立资源 复杂的知生系统仍然保留着定义机制的实验路径。