Computational and Experimental Resources for Virome Analysis in Inflammatory Bowel Disease (CERVAID)

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SUMMARY While the role of the bacterial microbiome in human health and disease is well established, few studies have evaluated the contribution of the virome. Recently, we demonstrated that alterations in the enteric virome in adulthood are associated with diseases such as inflammatory bowel disease (IBD) and AIDS. In a cross- sectional comparison of IBD cases and household controls, a significant expansion of the Caudovirales, an order of phages, and anelloviruses, a family of eukaryotic DNA viruses, was observed. Advancing understanding of the IBD virome beyond this finding is limited by: (1) A lack of well defined longitudinal human cohorts to enable discovery of temporal associations of the virome with health and disease; (2) The challenge of viral “dark matter”. Dark matter refers to the typically >50% of the sequences present in purified virus preparations cannot be classified due to a lack of statistically significant alignment to known reference sequences. Thus, current virome studies effectively assess < 50% of the virome, thereby compromising our ability to detect important associations between the virome and disease; (3) Inadequate experimental systems to manipulate the virome. Although sequencing has identified many novel eukaryotic viruses, there are only cell culture systems for a limited number of viruses; moreover, there are no small animal infection models for newly described viruses. In addition while a tremendous diversity of phage has been identified, only a tiny fraction have known hosts and an even smaller fraction has been cultured. Thus, there are significant barriers that must be overcome to be able to experimentally test the impact of either eukaryotic viruses or phages in murine IBD models. These barriers to understanding the role of the IBD virome will be addressed as follows: Aim 1 will define the enteric virome and bacterial microbiome in a longitudinal cohort of IBD patients and household controls and identify virome associations with IBD. In Aim 2 novel computational tools to identify and characterize viruses present in enteric viromes will be developed, including approaches to classify dark matter. In Aim 3 novel experimental systems for functional virome analysis, including novel cultures of both eukaryotic viruses and phages as well as animal infection models, will be developed with the end goal of evaluating causal roles for the viruses and phage in existing muring IBD models. Together, these Aims will not only address significant barriers in understanding of IBD, but will provide a wealth of tangible computational and experimental resources to advance the general field of virome studies.