Identification of antimicrobial specialized metabolites from the human oral microbiome to target multidrug-resistant pathogens

项目总结/摘要 我们的微生物组在定植抗性中起着关键作用，定植抗性是阻止生长、持久性和 随后被病原微生物感染。破坏已建立的微生物群落及其 功能可以改变感染易感性。了解口腔微生物组的变化如何使其 易受病原体定殖是必不可少的，因为耐药微生物的携带是 发展成严重和难以治疗的感染。我们的微生物群通过一种机制来防止 病原体定殖是通过产生抗菌特化代谢物（ASMs）， 抑制竞争微生物的生长。可通过以下方法促进此类生物活性代谢物的鉴定： 检测编码它们的生物合成基因簇（BGC）。生成的参考基因组的分析 通过人类微生物组项目，在不同的身体部位确定了3,118个BGC，其中典型的口腔 含有高BGC丰度（1，061 +/-143簇）的空腔。栖息在这里的微生物代表了 它是与环境和入侵微生物接触的第一点，因此发挥着至关重要的守门作用 防止病原体传播到下消化道和呼吸道。然而，结构和 由人类相关微生物群产生的ASM的功能仍然有限，特别是在口腔内。 该提案旨在利用比较宏基因组学和代谢组学方法的组合， 确定口腔相关细菌产生ASM在防御多重耐药中的作用 微生物（MDRO）。具体目标是：1）确定MDRO之间口腔微生物组的差异 携带者与非携带者，并评估健康的决定因素如何与丰富的关键 分类群，以及2）评估来自MDRO携带者的口腔相关细菌的生物活性ASM的产生 与非携带者相比。这些目标将通过鸟枪法宏基因组测序来实现。 来自不同人群的微生物组样本，结合与以下相关的详细相关元数据分析 健康和MDRO携带风险因素。将鉴定产生抗菌代谢物的细菌 通过高通量生物活性指导的分级分离，然后进行代谢组学分析和体内 功效测试研究口腔微生物群的ASM生产将深入了解形成这种情况的因素。 动态的微生物群落，并作为一个未开发的来源，急需的，新的抗菌药物的领导。 在威斯康星大学麦迪逊分校进行的无与伦比的微生物学研究将提供 一个理想的环境来开展拟议的工作。项目赞助商提供的资源和指导 博士卡梅隆柯里和合作者将促进及时完成这一建议。此外，执行 这项量身定制的研究培训计划将使申请人能够开发必要的实验， 沟通和临床技能，成功过渡到作为一个医生，科学家的职业生涯。

PROJECT SUMMARY / ABSTRACT Our microbiome plays a key role in colonization resistance, which is the prevention of growth, persistence, and subsequent infection by pathogenic microorganisms. Disruptions in an established microbial community and its functioning can alter infection susceptibility. Understanding how changes in the oral microbiome render it vulnerable to pathogen colonization is essential, as carriage of drug-resistant microbes is a major risk factor for developing serious and difficult-to-treat infections. One mechanism by which our microbiome acts to prevent pathogen colonization is through the production of antimicrobial specialized metabolites (ASMs) that directly inhibit the growth of competing microbes. Identification of such bioactive metabolites can be facilitated by examining the biosynthetic gene clusters (BGC) that encode them. Analysis of reference genomes generated through the Human Microbiome Project identified 3,118 BGCs across various body sites, with the typical oral cavity containing high BGC abundance (1,061+/-143 clusters). The microbiota inhabiting this site represent a first point of contact with the environment and invading microbes, and therefore, play a vital gatekeeping role against pathogen dissemination to the lower gastrointestinal and respiratory tracts. Yet, the structure and function of ASMs produced by human-associated microbiota remains limited, particularly within the oral cavity. This proposal seeks to leverage a combination of comparative metagenomic and metabolomic approaches to determine the role of ASM production by oral-associated bacteria in defense against multidrug-resistant organisms (MDRO). The specific aims are to 1) define differences in oral microbiomes between MDRO carriers versus non-carriers and assess how determinants of health associate with abundance of key taxa, and 2) evaluate the production of bioactive ASMs by oral-associated bacteria from MDRO carriers versus non-carriers. These objectives will be accomplished through shotgun metagenomic sequencing of oral microbiome samples from diverse populations, paired with analysis of detailed associated metadata relating to health and MDRO carriage risk factors. Identification of antimicrobial metabolite producing bacteria will be achieved through high-throughput bioactivity-guided fractionation, followed by metabolomic analysis and in vivo efficacy testing. The study of ASM production by oral microbiota will yield insight into the factors shaping this dynamic microbial community and serve as an untapped source for much-needed, new antimicrobial drug leads. The unmatched caliber of microbiology research performed at the University of Wisconsin-Madison will provide an ideal environment to carry out the proposed work. Resources and mentorship provided by project sponsor Dr. Cameron Currie and collaborators will facilitate the timely completion of this proposal. Moreover, execution of this tailored research training plan will enable the applicant to develop the necessary experimental, communication, and clinical skills for a successful transition to a career as a physician-scientist.