Although the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from those of adults. We find evidence for more than a 10-fold increase in the rate of evolution and strain turnover in the infant gut compared with healthy adults, with the mother–infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.

中文翻译：

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婴儿肠道微生物组的快速进化和应变更新

尽管已经对婴儿肠道微生物组的生态动力学进行了深入研究，但对婴儿肠道微生物组的进化动力学知之甚少。在这里，我们分析了 700 多名婴儿及其母亲在出生后第一年的纵向粪便宏基因组数据，发现婴儿肠道微生物组的进化动力学与成人不同。我们发现证据表明，与健康成人相比，婴儿肠道的进化率和应变转换率增加了 10 倍以上，分娩时的母婴过渡是基因丢失占主导地位的特别动态时期。在出生后的几个月内，这些动态稳定下来，并且随着微生物组的成熟，基因获得变得越来越频繁。我们进一步发现，婴儿的进化变化显示出由从头突变和来自更广泛家族的预进化谱系的传播混合播种的特征。这些进化变化中有几个在婴儿身上平行发生，突出了可能在婴儿肠道微生物组发育中发挥重要作用的候选基因。我们的结果指向一幅不稳定的婴儿肠道微生物群的图景，其特征是生命早期的快速进化和生态变化。