Harnessing macromolecules to study microbial (bio)chemical ecology

概况.细菌不是孤立的生物体：它们聚集成复杂的群落，建立在我们刚刚开始了解的非凡化学景观上。这些微生物群对于生物地球化学循环和动物发育都是必不可少的。由于固有的复杂性，了解特定的集体如何组装和运作特别具有挑战性。因此，改进提供这些细菌相互作用的分子细节的方法是一个主要的全球研究目标。该研究计划将开发新的发现管道，通过利用已知的生物系统来研究小分子，这些生物系统已经进化到促进化学交换。来自三种不同奶牛相关微生物组的细菌小分子将用于提供对细菌群落结构和功能的一般和特定见解。研究项目将开始与生物技术应用的大分子系统，相互作用和/或运输小分子。这种方法与传统的研究方案不同，传统的研究方案开始时采用粗糙的和一般化的提取方案。相反，我们将转向大分子的进化作用，以选择性地富集具有生态重要性的小分子。将开发两条研究管道。第一个将利用蛋白质-小分子相互作用来发现和分类铁载体，这是一种参与铁（一种必需的微量营养素）获取的小分子。第二部分将调查包裹在外膜囊泡（球形结构）中的抗生素，这些囊泡由革兰氏阴性菌分泌到环境中。强调进化的生物过程将提供显着减少化学复杂性的有机提取物，处理化学表征。通过简化我们的小分子分离管道，我们将加快发现新化合物的速度，并对已知结构进行编目，以更好地定义微生物冲突和合作中涉及的化学景观。总的来说，这两项开创性的研究将有助于开发一种新的模式，朝着微生物组的分子定义。除了将通过这项研究计划传播的培训和基础知识外，加拿大人还可能受益于新发现的小分子的未来治疗应用所带来的医药和经济潜力。特别是，目前市场上一半以上的药物都是直接利用小分子或启发合成的。虽然这些应用研究超出了本提案的范围，但我们将为未来的研究应用提供基础知识。

Overview. Bacteria are not solitary organisms: they assemble into complex communities built on extraordinary chemical landscapes that we are just beginning to understand. These microbiomes are as essential to biogeochemical cycles as they are to animal development. Due to the inherent complexity, understanding how specific collectives assemble and operate is particularly challenging. Thus, improving the approaches that provide access to the molecular details that underlie these bacterial interactions represents a major global research objective.This research proposal will develop new discovery pipelines to study small molecules by exploiting known biological systems that have evolved to facilitate chemical exchange. Bacterial small molecules from three distinct dairy cattle-associated microbiomes will be used to provide general and specific insight into bacterial community structure and function.Approach. Research projects will begin with biotechnological applications of macromolecular systems that interact with and/or transport small molecules. This approach is a departure from conventional research programs, which begin with crude and generalized extraction protocols. Instead, we will turn to the evolved roles of macromolecules to selectively enrich for ecologically important sets of small molecules. Two research pipelines will be developed. The first will leverage protein-small molecule interactions to discover and catalogue siderophores, small molecules that are involved in the acquisition of iron, an essential micronutrient. The second will survey antibiotics that have been encapsulated within outer-membrane vesicles - spherical structures - that are secreted by Gram-negative bacteria into their environment.Impact. The emphasis on evolved biological processes will afford remarkable reductions in the chemical complexity of organic extracts that are processed for chemical characterization. By simplifying our small molecule isolation pipeline, we will accelerate the rate at which new compounds are discovered and catalogue known structures to better define the chemical landscapes involved in microbial conflict and cooperation. Overall, these two pioneering studies will help to develop a new paradigm toward a molecular definition of microbiomes.In addition to the training and fundamental knowledge that will be disseminated by this research program, Canadians may also benefit from the medicinal and economic potential derived from future therapeutic applications of the newly discovered small molecules. In particular, small molecules are utilized directly or have inspired the synthesis of more than half of the drugs currently on the market. While these applied studies are beyond the scope of this proposal, we will provide foundational knowledge for future research applications.