Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1(Suppl 1):4578-85. doi: 10.1073/pnas.1000081107. Epub 2010 Jul 28.
The colonization process of the infant gut microbiome has been called chaotic, but this view could reflect insufficient documentation of the factors affecting the microbiome. We performed a 2.5-y case study of the assembly of the human infant gut microbiome, to relate life events to microbiome composition and function. Sixty fecal samples were collected from a healthy infant along with a diary of diet and health status. Analysis of >300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient. In contrast, major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health. Community assembly was nonrandom: we observed discrete steps of bacterial succession punctuated by life events. Furthermore, analysis of ≈ 500,000 DNA metagenomic reads from 12 fecal samples revealed that the earliest microbiome was enriched in genes facilitating lactate utilization, and that functional genes involved in plant polysaccharide metabolism were present before the introduction of solid food, priming the infant gut for an adult diet. However, ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes, elevated fecal short chain fatty acid levels, enrichment of genes associated with carbohydrate utilization, vitamin biosynthesis, and xenobiotic degradation, and a more stable community composition, all of which are characteristic of the adult microbiome. This study revealed that seemingly chaotic shifts in the microbiome are associated with life events; however, additional experiments ought to be conducted to assess how different infants respond to similar life events.
婴儿肠道微生物组的定植过程被称为混乱，但这种观点可能反映了对影响微生物组的因素记录不足。我们对人类婴儿肠道微生物组的组装进行了为期 2.5 年的案例研究，以将生活事件与微生物组的组成和功能联系起来。我们从一名健康婴儿身上收集了 60 份粪便样本，并附有一份饮食和健康状况日记。对超过 300,000 个 16S rRNA 基因的分析表明，微生物组的系统发育多样性随着时间的推移逐渐增加，群落组成的变化符合平滑的时间梯度。相比之下，主要的分类群的丰度突然发生变化，与饮食或健康状况的变化相对应。群落组装是无随机的：我们观察到细菌连续体的离散步骤，这些步骤由生活事件打断。此外，对 12 份粪便样本中约 500,000 个 DNA 宏基因组读数的分析表明，最早的微生物组富含促进乳酸利用的基因，并且植物多糖代谢相关的功能基因在固体食物引入之前就存在，为婴儿肠道适应成人饮食做好准备。然而，食用餐桌食物会导致拟杆菌门的丰度持续增加，粪便短链脂肪酸水平升高，与碳水化合物利用、维生素生物合成和外来化合物降解相关的基因富集，以及群落组成更加稳定，所有这些都是成人微生物组的特征。这项研究表明，微生物组中看似混乱的变化与生活事件有关；然而，应该进行更多的实验来评估不同的婴儿如何对类似的生活事件做出反应。
