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

总结 虽然细菌微生物组在人类健康和疾病中的作用已经得到了很好的确立，但很少有研究 评估了病毒组的贡献。最近，我们证明了肠道病毒组的改变 在成年期，与诸如炎症性肠病（IBD）和艾滋病等疾病有关。在十字架上- IBD病例和家庭对照的截面比较，尾状病毒目的显著扩展， 和真核DNA病毒家族的环节病毒。推进 对IBD病毒组的理解受到以下因素的限制：（1）缺乏明确的纵向人类基因组， 队列，以发现病毒组与健康和疾病的时间关联;（2）挑战 病毒性“暗物质”暗物质是指纯化病毒中存在的通常>50%的序列 由于与已知参比品缺乏统计学显著性一致性，因此无法对制剂进行分类 序列的因此，目前的病毒组研究有效地评估了< 50%的病毒组，从而损害了我们的研究。 检测病毒组和疾病之间重要关联的能力;（3）实验系统不足 来操纵病毒组尽管测序已经鉴定出许多新的真核病毒， 细胞培养系统的数量有限的病毒;此外，没有小动物感染模型， 新发现的病毒此外，虽然已经鉴定出了巨大的噬菌体多样性，但只有很少的噬菌体。 部分已经知道宿主，甚至更小的部分已经培养。因此， 必须克服这一点，才能在实验上测试真核病毒或病毒素的影响， 鼠IBD模型。这些理解IBD病毒组作用的障碍将如下所述： 目的1将定义IBD患者纵向队列中的肠道病毒组和细菌微生物组， 家庭控制和鉴定与IBD相关的病毒组。在Aim 2中， 并描述存在于肠道病毒组中的病毒，包括对黑暗病毒进行分类的方法。 所谓了在Aim 3中，用于功能性病毒组分析的新实验系统，包括两种病毒的新培养物， 真核病毒和病毒以及动物感染模型，将开发的最终目标是 评估病毒和噬菌体在现有的鸡传染性法氏囊病模型中的因果作用。总之，这些目标不会 仅解决了理解IBD的重大障碍，但将提供丰富的有形计算 和实验资源，以推进病毒组研究的一般领域。

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.