Fahur Bottino Guilherme, Bonham Kevin S, Patel Fadheela, McCann Shelley, Zieff Michal, Naspolini Nathalia, Ho Daniel, Portlock Theo, Joos Raphaela, Midani Firas S, Schüroff Paulo, Das Anubhav, Shennon Inoli, Wilson Brooke C, O'Sullivan Justin M, Britton Robert A, Murray Deirdre M, Kiely Mairead E, Taddei Carla R, Beltrão-Braga Patrícia C B, Campos Alline C, Polanczyk Guilherme V, Huttenhower Curtis, Donald Kirsten A, Klepac-Ceraj Vanja
Department of Biological Sciences, Wellesley College, Wellesley, MA, USA.
University of Cape Town, Cape Town, Western Cape, South Africa.
Nat Commun. 2025 Jan 14;16(1):660. doi: 10.1038/s41467-025-56072-w.
Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that may be used alongside other measures of child development.
了解婴儿肠道微生物群的群落演替动态对于理解儿童健康与发育至关重要,但目前尚无规范模型。在此,我们利用宏基因组中肠道微生物分类相对丰度来估算儿童年龄,在生命的前1.5年具有高时间分辨率(±3个月)。我们使用来自12个国家1827名婴儿的3154个样本,训练了一个随机森林模型,均方根误差为2.56个月。我们确定了年龄的关键分类预测因子,包括双歧杆菌属的减少以及普拉梭菌和毛螺菌科的增加。微生物演替模式在不同人群的婴儿中是保守的,这表明存在普遍的发育轨迹。功能分析证实了参与喂养转变和饮食暴露的关键微生物基因的趋势。该模型为评估早期肠道成熟提供了“微生物组年龄”的规范基准,可与其他儿童发育指标一起使用。