Understanding how bacteriophages affect wound ecologies and developing new tools to harness bacteria-phage interactions

细菌病原体对抗生素耐药性的惊人上升是一个主要的问题， 对有效治疗感染的挑战。一种可能的正交策略， 对付细菌病原体的方法是利用噬菌体（噬菌体）， 感染细菌，因此是细菌的天敌。很少有人知道的 与人类微生物一起生活的微生物，因为它们被称为“暗物质” 微生物生态学。然而，已知益生菌可以控制细菌种群， 海洋环境和怀疑遏制季节性流行的霍乱。一个 一个悬而未决的问题是抗生素是否会影响个体感染中的细菌种群。 这项提案的第一个目标是调查在自然的作用， 伤口的微生物组，使用三个系统：慢性伤口，伤口， 表面手术伤口微生物组，包括细菌，将被表征 寻找愈合状态、噬菌体数量和特定噬菌体之间的相关性， 物种被发现与愈合相关的噬菌体是有趣的靶点， 进一步的研究和工程。任何潜在的噬菌体为基础的重要相关方面 治疗的目的是了解噬菌体应用对整个微生物 生态因此，本项目的第二个目标是开发一个实验模型 的微生物生态系统，并扰乱这个生态系统使用特定的微生物， 特定的细菌种类。生态系统的反应将揭示 微生物群落中的生态相互作用。该分析将用于开发 噬菌体-细菌系统的模型。最后，特定噬菌体的安全应用 原则上，需要对该噬菌体的生物学进行大量研究， 不必要的相互作用，如基因转导。可替代地，混合型微处理器可以是 被开发以掺入来自相对未表征的细菌的所需基因（例如， 靶向特定细菌病原体的外壳蛋白）进入支架噬菌体， 其生物学特性是众所周知的，并且其安全性已经在前面描述过。因此 该项目的第三个目标是制定一个系统的方法来设计和 具有已知可控特性的工程混合动力发动机， 从噬菌体宏基因组的外壳蛋白到模型噬菌体M13。工作 这里提出的将有助于描绘基于噬菌体的替代品的潜力， 抗生素

The alarming rise of resistance to antibiotics among bacterial pathogens is a major challenge to the effective treatment of infections. A possible orthogonal strategy for countering bacterial pathogens is to make use of bacteriophages (phages), viruses that infect bacteria and are thus natural predators of bacteria. Little is known about the phages that live with the human microbiome, as they have been called the 'dark matter' of microbial ecology. However, phages are known to control bacterial populations in the marine environment and are suspected of curbing seasonal epidemics of cholera. An open question is whether phages affect bacterial populations in individual infections. The first goal of this proposal is to investigate the natural role of phages in the microbiome of wounds, using three systems: chronic wounds, abscesses, and superficial surgical wounds. The microbiome, including the phages, will be characterized to look for correlations between healing status, phage amount, and specific phage species. Phages that are found to correlate with healing are interesting targets for further study and engineering. An important related aspect of any potential phage-based therapy is to understand the consequences of phage application on the entire microbial ecology. Therefore, the second goal of this project is to develop an experimental model of a microbial ecosystem, and to perturb this ecosystem using phages specific for a particular bacterial species. The response of the ecosystem will reveal the underlying ecological interactions in the microbial community. This analysis will be used to develop a model of phage-bacteria systems. Finally, the safe application of a specific phage would, in principle, require considerable study of the biology of that phage to prevent unwanted interactions, such as gene transduction. Alternatively, hybrid phages may be developed to incorporate desirable genes from relatively uncharacterized phages (e.g., a coat protein targeted a particular bacterial pathogen) into a scaffold phage whose biology is well-known and whose safety has been previously described. Therefore, the third goal of this project is to develop a systematic approach to designing and engineering hybrid phages with known, controllable properties, based on incorporation of coat proteins from the phage metagenome into the model phage M13. The work proposed here will help delineate the potential of phage-based alternatives to antibiotics.