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

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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.