Gnotobiotics mice and bacterial cultures phenotyping core

项目摘要/摘要-核心C 寄主-微生物组研究的一个主要需求是开发可提供 了解肠道微生物对各种疾病的机制贡献的途径 参与进来。无菌小鼠被植入培养微生物的“合成群落”，提供 这样一条路径，如由此产生的“灵知的小鼠”，只包含已知身份的微生物，而且通常 基因组序列。然而，即使使用了培养和完全测序的微生物，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 培养微生物的表型鉴定有助于解决与后一点相关的知识鸿沟。 微生物表型和灵生生物模型核心的主要目标将是1。提供 培养和组合与抗性淀粉降解相关的现有微生物的资源， 丁酸盐生产、氢气消耗和胆盐水解；2.对 患者样本对抗性淀粉消费的反应不同，目的是建立模型 在寄生于隔离物种的诺生菌小鼠中的这些变异；以及3.进行代谢 表型和基因组测序相结合的分离微生物，以便他们的因果作用 抗性淀粉消耗对移植物抗宿主病和胆汁酸修饰的影响 肠球菌感染可以通过特定功能的透镜进行研究。在后一种情况下， 这些功能将包括被认为与拟议的结果直接相关的表型 疾病模型(抗性淀粉降解、丁酸生产和胆盐水解酶活性)。 然而，我们也预计将我们的表型测量扩展到定义其他代谢方面， 如微生物与膳食营养素的相互作用超越了抗性淀粉，这样我们就可以更好地 了解他们对社区行为、丁酸盐生产等的贡献。Marten实验室有 具有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)，从群体建立合成群落 具有明确表型和推动宿主疾病进展差异的微生物通过 外源力量对微生物区系的影响，如饮食。这一核心将是执行 在几个拟议的项目中进行试验，并将建立用于建立 复杂的灵知生菌系统，仍然保持着一条通往定义机制的实验道路。

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.