Systematic characterization of bioactive molecules from the human microbiome

摘要 人体微生物组和宿主之间存在复杂的相互作用，对人体的免疫系统产生明显的影响。 人体生理学和微生物生态学。一个有希望的途径来剖析这种相互作用， 机制水平是通过研究微生物组衍生的分子，介导重要的 微生物-微生物和微生物-宿主相互作用。在这个应用中，我们提出了一个混合计算- 用合成生物学方法发现、合理区分优先次序并系统地表征微生物组- 衍生分子我们建议将这种方法应用于三种结构不同的生物活性物质， 这些分子由人类微生物组广泛编码，但在人类中仍然严重缺乏研究。 从结构和功能两个方面。首先，以生物合成基因的计算分析为指导， 在来自数千名受试者的人类微生物组的宏基因组测序数据中， 将选择三种分子类别的特定成员进行实验表征。第二、 我们将在多宿主中使用微生物组天然成员的基因组编辑和合成生物学， 通过构建异源表达平台来表征所选择的途径及其产物。最后我们 将采用一系列体外、基于细胞的和小鼠定殖测定来询问 发现了介导相关宿主和微生物功能的分子。总的来说，我们的 这种方法将揭示人类微生物组与微生物之间相互作用的一个被破坏的部分。 宿主和提供多种微生物组衍生生物活性分子作为未来机制的工具 研究和治疗干预。

ABSTRACT A complex interplay exists between the human microbiome and the host, resulting in clear effects on human physiology and microbiome ecology. A promising avenue to dissect this interplay at a mechanistic level is through the study of microbiome-derived molecules that mediate important microbe-microbe and microbe-host interactions. In this application, we propose a hybrid computational- synthetic biology approach to discover, rationally prioritize and systematically characterize microbiome- derived molecules. We propose to apply this approach to three structurally diverse classes of bioactive molecules that are widely encoded by the human microbiome but remain severely understudied in terms of both structure and function. First, guided by the computational analysis of biosynthetic gene clusters in metagenomic sequencing data from the human microbiome of thousands of subjects, we will select specific members of the three molecular classes for experimental characterization. Second, we will use genome editing of native members of the microbiome and synthetic biology in a multi-host heterologous expression platform to characterize the selected pathways and their products. Finally, we will employ an array of in vitro, cell-based and mouse colonization assays to interrogate the role of the discovered molecules in mediating relevant host and microbiome functions. Taken together, our approach will unveil an undermined section of the interplay between the human microbiome and the host and provide diverse microbiome-derived bioactive molecules as tools for future mechanistic studies and therapeutic interventions.