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.

项目摘要/摘要 - 核心C 宿主 - 微生物组研究的主要需求是开发可拖动的模型系统 了解肠道微生物对各种疾病的机械贡献的途径 参与。植入培养的微生物的“合成群落”的无用小鼠提供 这样的路径诸如所产生的“ gnotobiotic小鼠”仅包含已知身份的微生物，并且经常包含 基因组序列。但是，即使使用了培养和完全测序的微生物，也是一个主要的 限制是了解所涉及的微生物的代谢潜力。高通量代谢 培养的微生物的表型有助于解决与后点相关的知识差距。 微生物表型和gnotobiotic模型核心的主要目标是1。 用于聚类和结合与抗性淀粉降解相关的现有微生物的资源， 丁酸盐的产生，H2消耗和胆汁盐水解； 2.对有针对性的深层文化 患者样品在对抗性淀粉消耗的反应中有所不同，目的是建模 用孤立物种定殖的gnotobiotic小鼠的这些变化；和3。执行代谢 表型结合在分离的微生物上结合基因组测序，以使它们的因果关系在 确定GVHD上抗性淀粉消耗的结果和胆汁酸修饰的结果 可以通过定义功能的镜头研究肠球菌感染。在后一种情况下， 这些功能将包括被认为直接涉及提案结果的表型 疾病模型（抗性淀粉，丁酸盐产生和胆汁盐水解酶活性的降解）。 但是，我们还预计将扩展表型测量以定义其他代谢方面， 例如与耐药淀粉以外的饮食营养物质的微生物相互作用，以便我们可以更好 了解他们对社区行为的贡献，丁丽酸酯的生产等。马滕斯实验室有 在自定义表型生长阵列中分析培养的人肠道细菌的丰富经验（例如 为了广泛测量多糖降解能力），从组中建立合成社区 具有定义表型的微生物和通过 饮食等微生物群上的外源力。该核心将是执行的基础 在拟议的几个项目中进行的实验，还将建立建造资源 复杂的gnotobiotic系统仍然保留了定义机制的实验途径。