Antibiotics from nose and throat commensals that impact pathogen colonization

描述（由申请人提供）：该提案基于一项长期且有趣的临床观察，该观察与人类健康直接相关，并涉及人类鼻子和喉咙微生物群落的动态：约50%的个体未定植金黄色葡萄球菌或肺炎链球菌，因此被这些重要病原体感染的风险较低。我们假设这些个体的鼻子和喉咙中有相互作用的产生抗生素的细菌，这些细菌选择性地抑制金黄色葡萄球菌和/或肺炎葡萄球菌的定植和增殖。我们最近的研究表明，在鼻孔中，杆状杆菌属和丙酸杆菌属的共生放线菌抑制金黄色葡萄球菌的定植。我们已经确定了这些定植阻断细菌的菌株，它们产生抑制金黄色葡萄球菌生长的小分子。这些有益微生物和它们产生的抗生素可以作为新型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子和喉咙微生物群落动力学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，这些样本是美国国立卫生研究院资助的肺炎链球菌携带研究的一部分。这一独特而有价值的样本集捕捉到了人类发展的一个阶段，当时金黄色葡萄球菌和肺炎葡萄球菌的携带在不断变化；肺炎链球菌携带率在学步期达到45%的峰值，此时金黄色葡萄球菌携带率处于10%的低点，随着儿童接近学龄，金黄色葡萄球菌携带率上升，到青春期达到30%。我们将采用一个多学科的策略，分为三个目标。在目标1中，我们将对现有的200对鼻孔和鼻咽微生物群样本进行深度测序，以确定哪些分类群与培养证实的金黄色葡萄球菌和肺炎葡萄球菌呈负相关，并进行共培养试验，以确定这些候选定植阻断细菌中哪些产生抗生素。在Aim 2中，我们将从Aim 1中使用生物测定引导分离纯化这些抗生素，并使用NMR和MS来解决它们的结构。在目标3中，我们将结合生物信息学和细菌遗传学来识别编码这些抗生素的基因，我们将测试是否

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.