Vertical transmission of bacteria from mother to infant at birth is postulated to initiate a life-long host-microbe symbiosis, playing an important role in early infant development. However, only the tracking of strictly defined unique microbial strains can clarify where the intestinal bacteria come from, how long the initial colonizers persist, and whether colonization by other strains from the environment can replace existing ones. Using rare single nucleotide variants in fecal metagenomes of infants and their family members, we show strong evidence of selective and persistent transmission of maternal strain populations to the vaginally born infant and their occasional replacement by strains from the environment, including those from family members, in later childhood. Only strains from the classes Actinobacteria and Bacteroidia, which are essential components of the infant microbiome, are transmitted from the mother and persist for at least 1 yr. In contrast, maternal strains of Clostridia, a dominant class in the mother's gut microbiome, are not observed in the infant. Caesarean-born infants show a striking lack of maternal transmission at birth. After the first year, strain influx from the family environment occurs and continues even in adulthood. Fathers appear to be more frequently donors of novel strains to other family members than receivers. Thus, the infant gut is seeded by selected maternal bacteria, which expand to form a stable community, with a rare but stable continuing strain influx over time.

据推测，出生时细菌从母亲到婴儿的垂直传播会引发终生的宿主-微生物共生，在婴儿早期发育中发挥重要作用。然而，只有追踪严格定义的独特微生物菌株才能弄清楚肠道细菌来自哪里、最初的定殖者持续多久，以及来自环境的其他菌株的定殖是否可以取代现有的菌株。利用婴儿及其家庭成员粪便宏基因组中的罕见单核苷酸变异，我们显示了强有力的证据，证明母体菌株群体选择性且持续地传播给阴道出生的婴儿，并且它们偶尔被环境菌株（包括来自家庭成员的菌株）取代。后来的童年。只有放线菌门和拟杆菌门的菌株（它们是婴儿微生物组的重要组成部分）才会从母亲传播并持续至少 1 年。相比之下，母体梭状芽胞杆菌菌株是母亲肠道微生物群中的优势类别，但在婴儿中却没有观察到。剖腹产婴儿出生时明显缺乏母体传播。第一年后，来自家庭环境的压力就会涌入，甚至在成年后还会持续。父亲似乎更频繁地向其他家庭成员提供新菌株，而不是接受者。因此，婴儿肠道被选定的母体细菌播种，这些母体细菌扩展形成一个稳定的群落，随着时间的推移，稀有但稳定的菌株持续流入。