Commensal gut bacterial communities (microbiomes) are predicted to influence human health and disease^1,2. Neonatal gut microbiomes are colonized with maternal and environmental flora and mature toward a stable composition over 2-3 years^3,4. To study pre- and postnatal determinants of infant microbiome development, we analyzed 402 fecal metagenomes from 60 infants aged 0-8 months, using longitudinal generalized linear mixed models (GLMMs). Distinct microbiome signatures correlated with breastfeeding, formula ingredients, and maternal gestational weight gain (GWG). Amino acid synthesis pathway accretion in breastfed microbiomes complemented normative breastmilk composition. Prebiotic oligosaccharides, designed to promote breastfed-like microflora⁵, predicted functional pathways distinct from breastfed infant microbiomes. Soy formula in six infants was positively associated with Lachnospiraceae and pathways suggesting a short-chain fatty acid (SCFA)-rich environment, including glycerol to 1-butanol fermentation, which is potentially dysbiotic. GWG correlated with altered carbohydrate degradation and enriched vitamin synthesis pathways. Maternal and postnatal antibiotics predicted microbiome alterations, while delivery route had no persistent effects. Domestic water source correlates suggest water may be an underappreciated determinant of microbiome acquisition. Clinically important microbial pathways with statistically significant dietary correlates included dysbiotic markers^6,7, core enterotype features⁸, and synthesis pathways for enteroprotective⁹ and immunomodulatory^10,11 metabolites, epigenetic mediators¹, and developmentally critical vitamins¹², warranting further investigation.

中文翻译：

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婴儿饮食和母亲妊娠期体重增加预测肠道微生物组的早期代谢成熟。


共生肠道细菌群落（微生物组）预计会影响人类健康和疾病^1,2 。新生儿肠道微生物群被母体和环境菌群定殖，并在 2-3 年内成熟为稳定的组成^3,4 。为了研究婴儿微生物组发育的产前和产后决定因素，我们使用纵向广义线性混合模型 (GLMM) 分析了 60 名 0-8 个月婴儿的 402 个粪便宏基因组。独特的微生物组特征与母乳喂养、配方奶粉成分和母亲妊娠期体重增加 (GWG) 相关。母乳喂养的微生物组中氨基酸合成途径的增加补充了正常的母乳成分。益生元寡糖旨在促进类似母乳喂养的微生物群⁵ ，预测了与母乳喂养的婴儿微生物组不同的功能途径。六名婴儿的大豆配方奶粉与 Lachnospiraceae 和途径呈正相关，表明富含短链脂肪酸 (SCFA) 的环境，包括甘油发酵为 1-丁醇，这可能是菌群失调。 GWG 与改变的碳水化合物降解和丰富的维生素合成途径相关。孕产妇和产后抗生素可预测微生物组的变化，而分娩途径没有持续影响。国内水源相关性表明水可能是微生物组获取的一个未被充分认识的决定因素。 临床上重要的微生物途径与统计上显着的饮食相关性包括生态失调标记物^6,7 、核心肠型特征⁸以及肠道保护性⁹和免疫调节代谢物^10,11的合成途径、表观遗传介质¹和发育关键维生素¹² ，值得进一步研究。