Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.

噬菌体是肠道微生物群的关键组成部分，但噬菌体在婴儿肠道中的定植过程仍不确定。在这里，我们建立了一个大型噬菌体序列数据库，并使用菌株解析分析来研究婴儿生命前 3 年的 DNA 噬菌体演替情况。对从 28 名足月婴儿和 24 名早产儿及其母亲收集的 819 个粪便宏基因组进行的分析表明，早期噬菌体丰富度随着时间的推移而增加，并在 3 岁时达到成人样的复杂性。大约 9% 的早期噬菌体定殖者，其中大部分是母体传播和感染拟杆菌，持续 3 年，足月儿比早产儿更常见。虽然很少见，但具有终止密码子重新分配的噬菌体比未重新编码的噬菌体更有可能持续存在，并且通常在 3 年内表现出框内重新分配的终止密码子的增加。总体而言，母体播种、终止密码子重新分配、宿主 CRISPR-Cas 位点流行以及多样化的噬菌体群体有助于稳定的病毒定植。