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

摘要 虽然细菌微生物群在人类健康和疾病中的作用已经得到了很好的证实，但很少有研究 已经评估了病毒的贡献。最近，我们证明了肠道病毒群的变化 在成年期与炎症性肠病(IBD)和艾滋病等疾病有关。在十字架上- IBD病例和家庭对照的横断面比较，尾状病毒属的显著扩大，以及 噬菌体和针状病毒是真核DNA病毒的一个家族。前进 除了这一发现之外，对IBD病毒体的理解受到以下限制：(1)缺乏明确定义的纵向人类 能够发现病毒体与健康和疾病之间的时间关联的队列；(2)挑战 病毒一样的“暗物质”。暗物质指的是通常存在于纯化病毒中的50%的序列 由于缺乏与已知参考文献的统计显著比对，不能对制剂进行分类 序列。因此，目前的病毒研究有效地评估了50%的病毒，从而损害了我们的 检测病毒体和疾病之间重要联系的能力；(3)实验系统不足 来操控病毒。尽管测序已经发现了许多新的真核病毒，但只有 细胞培养系统用于有限数量的病毒；此外，没有小动物感染模型 新描述的病毒。此外，虽然已经发现了种类繁多的噬菌体，但只有一小部分 其中一部分人知道宿主，培养出来的比例更小。因此，存在着巨大的障碍 必须克服这一点，才能在实验中测试真核病毒或噬菌体对 小鼠IBD模型。这些理解IBD病毒体作用的障碍将被解决如下： 目标1将确定IBD患者纵向队列中的肠道病毒群和细菌微生物群 家庭控制和确定病毒与IBD的关联。在目标2中，使用新的计算工具来识别 将开发肠道病毒中存在的病毒的特征，包括对黑暗进行分类的方法 物质。在AIM中，3个用于功能病毒体分析的新实验系统，包括两者的新培养物 将开发真核病毒和噬菌体以及动物感染模型，最终目标是 评估病毒和噬菌体在现有小鼠IBD模型中的因果作用。加在一起，这些目标不会 仅解决了理解IBD方面的重大障碍，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.