The human gut virome is thought to significantly impact the microbiome and human health. However, most virome analyses have been performed on a limited fraction of known viruses. Using whole-virome analysis on a published keystone inflammatory bowel disease (IBD) cohort and an in-house ulcerative colitis dataset, we shed light on the composition of the human gut virome in IBD beyond this identifiable minority. We observe IBD-specific changes to the virome and increased numbers of temperate phage sequences in individuals with Crohn’s disease. Unlike prior database-dependent methods, no changes in viral richness were observed. Among IBD subjects, the changes in virome composition reflected alterations in bacterial composition. Furthermore, incorporating both bacteriome and virome composition offered greater classification power between health and disease. This approach to analyzing whole virome across cohorts highlights significant IBD signals, which may be crucial for developing future biomarkers and therapeutics.

人们认为肠道病毒会严重影响微生物组和人类健康。但是，大多数病毒分析已对有限比例的已知病毒进行了分析。通过对已发表的关键性结石性炎症性肠病（IBD）队列和内部溃疡性结肠炎数据集进行全病毒组分析，我们发现了这一可识别的少数人群之外，IBD中人肠道病毒的组成。我们观察到克罗恩病患者中IBD的病毒特异性变化和温带噬菌体序列的数量增加。与以前的依赖数据库的方法不同，没有观察到病毒丰富度的变化。在IBD受试者中，病毒组成的变化反映了细菌组成的改变。此外，结合了细菌学和病毒组成，在健康和疾病之间提供了更大的分类能力。这种分析整个人群的整个病毒的方法突出了重要的IBD信号，这可能对开发未来的生物标志物和治疗方法至关重要。