Uncovering the roles of phages in the ecology of Porphyromonas gingivalis in periodontal disease

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PROJECT SUMMARY/ABSTRACT The broad goal of the proposed work is to address the lack of knowledge about the roles of bacterial viruses (phages) in shaping the ecology of oral microbial communities. Phages are important predators and symbionts of bacteria in all environments, and they are abundant in the oral cavity (up to 108 ml-1 in saliva and 107 mg-1 plaque). Through acute and chronic infections of their bacterial hosts, phages have the potential to shape bacterial population structure, colonization dynamics, and strain level variation in virulence. Yet, though bacteria in the oral microbiome have been studied for decades, little is known about how phages shape the structure and function of these communities and thereby may play a role in human health and disease. In this application, a bacterial pathogen that has been – and continues to be - intensively studied for its role as keystone species and driver in periodontal disease, Porphyromonas gingivalis (Pg), is developed as a model for studying bacteria-phage interactions in the oral microbiome. To date, no phages able to infect or kill Pg have been isolated, nor have Pg genomes been systematically investigated for evidence of chronically infecting forms of phages (“prophages”). The central hypothesis of the proposed work is that Pg isolates harbor diverse phages integrated into their genomes as prophages, and that these prophages have the potential to alter the ecology of Pg in the oral microbiome. Two complementary aims, providing both breadth and depth of insight into the roles of phages in the ecology of Pg, are used to address this hypothesis. In Aim 1, the goal is to identify and functionally characterize prophages encoded in genomes of Pg. This is achieved by obtaining new isolates of Pg from volunteers with periodontal disease to expand the number of available Pg genomes, and bioinformatically identifying and characterizing prophages in these genomes, including with respect to their capacity to contribute to bacterial virulence and intraspecies competition. In Aim 2, the goal is to determine the receptors used by prophages to infect their Pg hosts. This is achieved by establishing model systems of Pg phages and using cultivation based methods to identify their host range determinants. Completion of these aims will provide the first view of the phylogenetic and functional diversity of Pg phages, insights into their host ranges, and the first identification of receptors that they use to infect their Pg hosts. This will provide the research community with the knowledgebase and tools necessary to test hypotheses (in vitro, in vivo, and in longitudinal and cross-sectional studies) that address how interactions with phages shape Pg genomes, physiology, population dynamics, inter-species and inter-kingdom interactions, and role in periodontal disease and its progression. Uncovering fundamental principles of how phage-bacteria interactions are structured in the oral microbiome will also lay an essential foundation for the rational design of robust, safe, and efficient phage-based therapeutics for use in oral and systemic disease including periodontal disease.