Gnotobiotics mice and bacterial cultures phenotyping core

项目总结/摘要-核心C 宿主微生物组研究的主要需求是开发易于处理的模型系统， 一条了解肠道微生物对各种疾病的机制贡献的途径， 参加植入培养微生物的“合成群落”的无菌小鼠， 这样的路径作为所产生的“无菌小鼠”仅包含已知身份的微生物 基因组序列然而，即使使用培养和完全测序的微生物， 局限性在于了解所涉及的微生物的代谢潜力。高通量代谢 培养微生物的表型分析有助于解决与后一点相关的知识差距。 微生物表型分析和知生菌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消耗和胆盐水解; 2.对以下方面进行有针对性的深度培养： 患者样本对抗性淀粉消耗的反应不同， 在用分离的物种定殖的无菌小鼠中的这些变化;和3.执行代谢 表型分析与基因组测序相结合对分离的微生物， 确定抗性淀粉消耗对GVHD的影响和胆汁酸修饰对GVHD的影响， 肠球菌感染可以通过定义函数的透镜来研究。在后一种情况下， 这些功能将包括被认为直接涉及所提出的治疗结果的表型。 疾病模型（抗性淀粉降解、丁酸盐产生和胆盐水解酶活性）。 然而，我们也期望扩展我们的表型测量来定义其他代谢方面， 例如微生物与抗性淀粉以外的膳食营养素的相互作用， 了解它们对社区行为、丁酸盐生产等的贡献。 在定制表型生长阵列中测定培养的人肠道细菌的丰富经验（例如， 用于广泛测量多糖降解能力）， 具有确定表型的微生物，并通过以下方式驱动宿主疾病进展的差异： 微生物群上的外源性力量，如饮食。这一核心将是执行 在几个拟议的项目中进行实验，并将建立建设资源， 复杂的知生系统，仍然保留着一条通往定义机制的实验路径。

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.