The application of bacteriophages (phages) is proposed as a highly specific therapy for intestinal pathobiont elimination. However, the infectious associations between phages and bacteria in the human intestine, which is essential information for the development of phage therapies, have yet to be fully elucidated. Here, we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriomes), in 101 healthy Japanese individuals. Based on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-phage associations are illustrated for both temperate and virulent phages. To verify the usefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activity is confirmed both in vitro and in vivo. These comprehensive metagenome analyses reveal not only host bacteria-phage associations in the human intestine but also provide vital information for the development of phage therapies against intestinal pathobionts.

提出将噬菌体（噬菌体）的应用作为消除肠道病原体的高度特异性的疗法。然而，尚未充分阐明人肠中噬菌体和细菌之间的传染性关联，这是开发噬菌体疗法的重要信息。在这里，我们报告了101名健康的日本人的肠道病毒微生物组（病毒组）以及细菌微生物组（细菌组）。基于来自相同粪便样品的细菌群和病毒体的基因组序列，说明了温和噬菌体与宿主细菌-噬菌体的关联。为了验证全面的宿主细菌噬菌体信息的有用性，我们筛选了艰难梭菌特异性噬菌体和已鉴定的抗菌酶，其活性在体外和体内均得到证实。这些全面的基因组分析不仅揭示了人类肠道中宿主细菌与噬菌体的关联，而且还为开发针对肠道病原体的噬菌体疗法提供了重要信息。