Impact of Gut Bacterial Interactions on the Response to Fiber-Based Prebiotics

项目摘要/摘要 肠道微生物区系已经与人类健康的许多特征联系在一起，催生了开发 微生物区系导向疗法或益生元。确定安全、有效操作的策略/试剂 微生物区系的研究是当前精准医学倡议的一个高度优先目标。实现这一目标需要 描述益生元对肠道微生物影响的大小和机制的信息临床前模型 和寄主生物学，并对肠道群落动态有一个基本的了解。纤维类食品 已被证明对健康有有益的微生物介导的影响。了解膳食纤维如何 产生这些效应的原因是：(I)它们的成分复杂(例如，什么是生物活性 多聚糖？)，(Ii)对哪些细菌使用纤维中的特定组成多聚糖的知识有限，以及(Iii)竞争 以及细菌之间在这些多糖上的合作。我假设多糖组分 纤维和肠道群落成员的相互作用决定了对以纤维为基础的益生元的反应。 对这些相互作用及其潜在机制的了解，将有助于改进 微生物区系导向疗法。 我计划在一系列实验目标中检验这一假设。目标1将确定光纤依赖 由测序、培养的细菌菌株组成的模型人类肠道微生物区系中的细菌相互作用 安装在灵知生菌小鼠体内。我将系统地从这个模型社区中省略细菌，在它的 向小鼠介绍一种具有代表性的低纤维高饱和脂肪美国饮食补充 用一种纯净的植物性膳食纤维。我将分析社区操纵/纤程的影响 补充细菌基因表达和丰度。使用正向遗传筛选(全基因组 转座子突变文库)和基于质谱学的蛋白质组学和代谢组学，我将表征 细菌纤维反应的遗传决定因素和纤维制剂的生物活性成分 在信息丰富的社区环境中。目标2将通过一种新的方式扩展这些共生/多组学研究 使用CRISPR技术，允许选择性地从已建立的 在补充纤维的饮食环境中的社区。这项工作将加深我们对微生物区系功能的理解 以及我们如何才能推动一个社区走向稳定、有益的状态。我将生成并分析许多 多组数据集，同时接受人类微生物组领先研究人员的出色科学培训 科学和计算生物学。共同努力，以及由 这项提议将帮助我发展成为一名独立的内科科学家。

Project Summary/Abstract The gut microbiota has been linked to many features of human health, spawning efforts to develop microbiota-directed therapeutics or prebiotics. Identifying strategies/reagents for safe, efficacious manipulation of the microbiota is a high priority goal of current precision medicine initiatives. Achieving this goal requires informative preclinical models to describe the magnitude and mechanism of prebiotics’ effects on gut microbes and host biology, and to obtain a fundamental understanding of gut community dynamics. Fiber-based foods have been shown to have beneficial microbially-mediated effects on health. Understanding how dietary fibers produce these effects is confounded by (i) their compositional complexity (e.g., what are the bioactive glycans?), (ii) limited knowledge of which bacteria use specific constituent glycans in fiber, and (iii) competition and cooperation between bacteria over these glycans. I hypothesize that the polysaccharide components of fibers and gut community membership interact to dictate responses to fiber-based prebiotics. Knowledge of these interactions, and their underlying mechanisms, will inform development of improved microbiota-directed therapeutics. I plan to test this hypothesis in a series of experimental aims. AIM 1 will identify fiber-dependent bacterial interactions in a model human gut microbiota composed of sequenced, cultured bacterial strains installed in gnotobiotic mice. I will systematically omit bacteria from this model community prior to its introduction into mice fed a representative ‘unhealthy’ low fiber high saturated fat USA diet ± supplementation with a purified plant-derived dietary fiber. I will analyze the effects of community manipulation/fiber supplementation on bacterial gene expression and abundance. Using forward genetic screens (whole genome transposon mutant libraries) and mass spectrometry-based proteomics and metabolomics, I will characterize the genetic determinants of bacterial fiber responses and the bioactive components of fiber preparations across informative community contexts. AIM 2 will extend these gnotobiotic/multi-omic studies through a novel use of CRISPR technology that allows for selective depletion of targeted bacteria from an established community in a fiber-supplemented diet context. This work will refine our understanding of microbiota function and how we might drive a community toward stable, beneficial states. I will generate and analyze many multi-omic datasets while receiving excellent scientific training from leading researchers in human microbiome science and computational biology. Together, with the stellar clinical mentorship and training provided by Washington University SOM, this proposal will help me to develop into an independent physician-scientist.