Project Summary / Abstract Genomic methods have catalyzed a renaissance in the way that microorganisms are being studied. Previously, most knowledge of microbial processes and functions was obtained from a very limited number of tractable genetic systems. In contrast, current focus on microbiomes has shifted emphasis towards understanding a broad diversity of lifeforms that are only known from sequences and whose functions are inferred by homology to known or characterized organisms. Among the primary goals of our research program is to bridge these two approaches by adopting genomic, computational and experimental methods that directly test the roles, functions and adaptations of the non-model organisms that predominate in microbiomes. The first of the three Subject Areas proceeds from our findings that not only is there a high degree of host species-specificity in the contents of gut microbiomes but certain bacterial lineages have been co-diversifying with their hosts over millions of years. We will investigate how this co-diversification has progressed within the human population, and determine if and how these co-diversifying bacteria interact with hosts by testing their adaptive role in a dietary trait that is subject to strong selection in humans. We will also gain insights into the evolutionary history of the human microbiome by analyzing the new resolved strain-level variation detected in microbiome in a population genetics framework. The second Subject Area asks how new genes and functions originate in bacterial genomes. Most models of new gene formation are based on the duplication and modification of existing genetic information, and ignore the more fundamental question about how completely new genes can arise de novo. Whereas in eukaryotes, non-coding sequences seem to serve as templates for de novo gene origination, in bacteria there is strong, though indirect, evidence that phage may be the inventive source of new genes. The proposed research will determine the mechanisms by which new genes originate by testing the functional relevance and beneficial effects conferred by new viral sequences integrated into bacterial genomes. The third Subject Area proposes to address several questions concerning the role of viruses in microbial communities using a newly developed experimental system derived from viruses known previously only from metagenomic sequences. This system will allow us to resolve issues relating to viral host ranges, lifestyles and interactions—all questions that would remain as inferences, or wholly unanswered, if only genome sequences are available. Finally, we our plan to define the limits of gene exchange among viruses both to establish uniformity in their classification into meaningful biological units and to understand the potential for strains with new etiologies, distributions, and host tropisms to emerge.