Computational tools for illuminating the dark matter of the human virome

Project Summary As greater understanding of the important role that the human microbiome plays in human health has unfolded it is increasingly recognized that there is a vast and uncharted group of viruses that have direct and important influence on the composi�on, dynamics, and func�on of these microbial communi�es, and thus on the health of the human host. Metagenome sequencing efforts and other high-throughput methodologies have opened the door to large- scale cataloguing and characteriza�on of free-living viruses and prophage, which are resident in their bacterial host genomes. However, the diversity and lack of knowledge about these viruses hampers our ability to understand their poten�al impact. Illumina�ng the region outside of our current knowledge, so-called ‘dark mater’, is necessary to be able to understand, monitor, control, and u�lize virus-community interac�ons to promote human health. We hypothesize that applica�on of established and newly developed pipelines using these and other tools will allow vastly improved iden�fica�on and characteriza�on of viral elements that are impac�ng human microbiome dynamics, and that providing improved tools for visualizing these predic�ons and the rela�onships between them will have a broad impact on the field. To address these gaps we will develop enhanced methods for detec�on of viral sequences using graph assemblies, build a sequence- and structure-based pipeline for characteriza�on of auxiliary genes carried by viruses, and provide novel and useful ways of visualizing this complex informa�on to allow greater insight from researchers in the field.