Antibiotics from nose and throat commensals that impact pathogen colonization

描述（由申请方提供）：本提案基于长期且有趣的临床观察，该观察与人类健康直接相关，并涉及人类鼻和喉微生物群落的动态：约50%的个体未定植金黄色葡萄球菌或肺炎链球菌，因此这些重要病原体感染的风险较低。我们假设这些个体在他们的鼻子和喉咙里藏着互惠共生的产寄生虫细菌，它们选择性地抑制了沙门氏菌的定植和增殖。金黄色葡萄球菌和/或S.肺炎。我们最近的工作表明，在鼻孔中，棒状杆菌属和丙酸杆菌属的鼻腔放线菌抑制S。金黄色。我们已经鉴定出这些能产生抑制沙门氏菌的小分子的定植阻断细菌菌株。金黄色葡萄球菌生长这些有益的微生物和它们产生的抗生素可以作为新的小分子和益生菌疗法的基础。了解小分子介导的相互作用在鼻和喉微生物群落动态中的作用，将使我们能够制定预防和/或消除病原体携带的策略，从而大大降低感染的风险。为了验证这一假设，我们利用了一组独特的微生物群样本，这些样本已经作为NIH资助的S。肺炎携带这个独特而有价值的样本集捕捉了人类发展的一个阶段，当S。金黄色葡萄球菌和pneumoniae是一种流动的细菌;肺炎链球菌携带率在幼儿中最高约为45%，此时S.金黄色葡萄球菌的携带率较低，约为10%，然后是S.金黄色葡萄球菌携带率随着儿童接近学龄而上升，到青春期达到约30%。我们将采用多学科的战略，分为三个目标。在目标1中，我们将使用现存的200对鼻咽和鼻咽微生物群样本的深度测序来确定哪些分类群与培养证实的S.金黄色葡萄球菌和肺炎，以及共培养测定以鉴定这些候选定殖阻断细菌中的哪一种产生抗生素。在目标2中，我们将使用生物测定引导的分级分离来纯化来自目标1的这些抗生素，并使用NMR和MS来解析它们的结构。在目标3中，我们将使用生物信息学和细菌遗传学的组合来识别编码这些抗生素的基因，我们将测试这些基因是否具有生物学活性。 大肠杆菌编码基因的存在与S.金黄色葡萄球菌和在来自人类微生物组项目样品的社区宏基因组数据中，我们的努力将确定新的抗生素，调节鼻子和喉咙微生物群落动态和影响定植和感染的两个重要的细菌病原体：S。金黄色葡萄球菌和肺炎。

DESCRIPTION (provided by applicant): This proposal is based on a long-standing and intriguing clinical observation that is directly relevant to human health and concerns the dynamics of human nose and throat microbial communities: about 50% of individuals are not colonized with either Staphylococcus aureus or Streptococcus pneumoniae, and are consequently at low risk for infection by these important pathogens. We hypothesize that these individuals harbor mutualistic antibiotic-producing bacteria in their nose and throat that selectively inhibit the colonization and proliferation of S. aureus and/or S. pneumoniae. Our recent work suggests that in the nostrils, commensal Actinobacteria of the genera Corynebacterium and Propionibacterium inhibit colonization by S. aureus. We have identified strains of these colonization-blocking bacteria that produce small molecules that inhibit S. aureus growth. These beneficial microbes-and the antibiotics they produce-could serve as the basis for novel small molecule and probiotic therapies. An understanding of the role of small-molecule-mediated interactions in the dynamics of nose and throat microbial communities will allow us to develop strategies for preventing and/or eliminating pathogen carriage, drastically decreasing the risk for infection. To test this hypothesis, we take advantage of a unique set of microbiota samples already collected as part of an NIH-funded study of S. pneumoniae carriage. This unique and valuable sample set captures a stage of human development when carriage of S. aureus and S. pneumoniae is in flux; S. pneumoniae carriage rates peak at ~45% in toddlers, a time when S. aureus carriage rates are at a low of ~10%, then S. aureus carriage rates rise as children approach school age reaching ~30% by adolescence. We will use a multi-disciplinary strategy broken down into three aims. In Aim 1, we will use deep sequencing of an extant set of 200 paired nostril and nasopharyngeal microbiota samples to determine which taxa are inversely related with culture-proven S. aureus and S. pneumoniae, and co-culture assays to identify which of these candidate colonization-blocking bacteria produce an antibiotic. In Aim 2, we will use bioassay-guided fractionation to purify these antibiotics from Aim 1 and NMR and MS to solve the their structures. In Aim 3, we will use a combination of bioinformatics and bacterial genetics to identify the genes that encode these antibiotics and we will test whether the presence of antibiotic-encoding genes is negatively correlated with the presence of S. aureus and S. pneumoniae in community metagenomic data from Human Microbiome Project samples. Our efforts will identify new antibiotics that modulate nose and throat microbial community dynamics and impact colonization and infection by two important bacterial pathogens: S. aureus and S. pneumoniae.