Initial microbial colonization and later succession in the gut of human infants are linked to health and disease later in life. The timing of the appearance of the first gut microbiome, and the consequences for the early life metabolome, are just starting to be defined. Here, we evaluated the gut microbiome, proteome and metabolome in 88 African-American newborns using faecal samples collected in the first few days of life. Gut bacteria became detectable using molecular methods by 16 h after birth. Detailed analysis of the three most common species, Escherichia coli, Enterococcus faecalis and Bacteroides vulgatus, did not suggest a genomic signature for neonatal gut colonization. The appearance of bacteria was associated with reduced abundance of approximately 50 human proteins, decreased levels of free amino acids and an increase in products of bacterial fermentation, including acetate and succinate. Using flux balance modelling and in vitro experiments, we provide evidence that fermentation of amino acids provides a mechanism for the initial growth of E. coli, the most common early colonizer, under anaerobic conditions. These results provide a deep characterization of the first microbes in the human gut and show how the biochemical environment is altered by their appearance.

中文翻译：

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细菌定殖可重新编程新生儿肠道代谢组。

最初的微生物定植和后来在人类肠道中的继代与生命后期的健康和疾病有关。第一个肠道微生物组出现的时间以及对早期生命代谢组的影响才刚刚开始确定。在这里，我们使用生命的前几天收集的粪便样本评估了88名非裔美国人新生儿的肠道微生物组，蛋白质组和代谢组。出生后16 h，可以使用分子方法检测肠道细菌。对三种最常见物种，即大肠杆菌，粪肠球菌和寻常型拟杆菌的详细分析未表明新生儿肠道菌落的基因组特征。细菌的出现与大约50种人类蛋白质的丰度降低有关，游离氨基酸水平降低，细菌发酵产物（包括乙酸盐和琥珀酸盐）增加。使用流量平衡模型和体外实验，我们提供了氨基酸发酵为厌氧条件下大肠杆菌（最常见的早期定植菌）的初始生长提供了一种机制的证据。这些结果提供了人类肠道中第一种微生物的深入表征，并显示了其外观如何改变生化环境。