► Clooney AG, Sutton TDS, Shkoporov AN, et al. Wholevirome analysis sheds light on viral dark matter in IBD. Cell Host Microbe 2019;26:1–15. Analysing whole virome signatures within the human gut is the next major step in the field of the gut microbiome. To date, most virome analyses have detailed only a limited fraction of known viruses. However, it is estimated that the identifiable fraction of the virome can be as little as 15%, leaving approximately 85% of ‘dark matter’. In the context of IBD, increased overall virome diversity with a specific increase in Caudovirales abundance has been demonstrated in several studies. Clooney and colleagues aimed to make sense of the dark matter by revisiting a previously published keystone dataset (Norman, 2014) using a databaseindependent approach. This assembles the short metagenomic reads to resolve viral genomes and to determine their relative abundance. This allowed the authors to describe compositional change across the whole virome. By using this approach, they were able to show that a predominantly virulent core virome is linked to a healthy gut, with a shift from lysogenic to lytic replication in the temperate phage population in IBD. They did not confirm previous reports of a loss in overall viral diversity, with virome changes appearing to reflect bacterial compositional changes. Furthermore, incorporating both datasets into a disease classifier model offered improved patient group stratification, which they validated using a longitudinal cohort of patients with UC. The findings demonstrate a significant step forward in understanding the virome and its contribution to health and disease. This knowledge and capability will be vital in our continued search for future therapeutic strategies for IBD.

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文献中的 GI 亮点

► Clooney AG、Sutton TDS、Shkoporov AN 等。全病毒组分析揭示了 IBD 中的病毒暗物质。细胞宿主微生物 2019；26:1-15。分析人类肠道内的整个病毒组特征是肠道微生物组领域的下一个重要步骤。迄今为止，大多数病毒组分析仅详细说明了已知病毒的有限部分。然而，据估计，病毒组的可识别部分可以低至 15%，留下大约 85% 的“暗物质”。在 IBD 的背景下，在一些研究中已经证明了整体病毒组多样性的增加以及尾病毒目丰度的特定增加。Clooney 及其同事旨在通过使用独立于数据库的方法重新访问先前发布的 Keystone 数据集（Norman，2014）来理解暗物质。这组装了短的宏基因组读数以解析病毒基因组并确定它们的相对丰度。这使作者能够描述整个病毒组的组成变化。通过使用这种方法，他们能够证明主要毒力的核心病毒组与健康的肠道有关，在 IBD 的温带噬菌体群体中，从溶原复制到裂解复制。他们没有证实先前关于整体病毒多样性丧失的报告，病毒组变化似乎反映了细菌组成的变化。此外，将两个数据集合并到疾病分类器模型中可以改进患者组分层，他们使用 UC 患者的纵向队列对其进行了验证。这些发现表明在了解病毒组及其对健康和疾病的贡献方面向前迈出了重要一步。这种知识和能力对于我们继续寻找 IBD 未来的治疗策略至关重要。