Early life microbial succession in the gut follows common patterns in humans across the globe
Guilherme Fahur Bottino, Kevin S. Bonham, Fadheela Patel, Shelley McCann, Michal R. Zieff, Nathalia Ferrazzo Naspolini, Daniel Ho, Theo Portlock, Raphaela Joos, Firas S. Midani, Paulo Alfonso Schüroff, Anubhav Das, Inoli Shennon, Brooke C. Wilson, Justin M. O’Sullivan, Robert A. Britton, Deirdre M. Murray, Máiréad Kiely, Carla R. Taddei, Patrícia Cristina Baleeiro Beltrão-Braga, Alline C. Campos, Guilherme V. Polanczyk, Curtis Huttenhower, Kirsten A. Donald, Vanja Klepac‐Ceraj
Abstract
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. Here, the authors perform a global analysis of over 3000 infant gut samples revealing a universal pattern of microbial changes over the first 1.5 years, with declines in Bifidobacterium and increases in Faecalibacterium, providing a standard for early gut development.