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Early life microbial succession in the gut follows common patterns in humans across the globe

Author

Listed:
  • Guilherme Fahur Bottino

    (Wellesley College)

  • Kevin S. Bonham

    (Wellesley College)

  • Fadheela Patel

    (University of Cape Town)

  • Shelley McCann

    (Wellesley College)

  • Michal Zieff

    (University of Cape Town)

  • Nathalia Naspolini

    (University of São Paulo)

  • Daniel Ho

    (The University of Auckland)

  • Theo Portlock

    (The University of Auckland)

  • Raphaela Joos

    (APC Microbiome Ireland
    University College Cork)

  • Firas S. Midani

    (Baylor College of Medicine
    Baylor College of Medicine)

  • Paulo Schüroff

    (University of São Paulo)

  • Anubhav Das

    (APC Microbiome Ireland
    University College Cork)

  • Inoli Shennon

    (The University of Auckland)

  • Brooke C. Wilson

    (The University of Auckland)

  • Justin M. O’Sullivan

    (The University of Auckland)

  • Robert A. Britton

    (Baylor College of Medicine
    University College Cork)

  • Deirdre M. Murray

    (University College Cork)

  • Mairead E. Kiely

    (University College Cork)

  • Carla R. Taddei

    (University of São Paulo)

  • Patrícia C. B. Beltrão-Braga

    (University of São Paulo)

  • Alline C. Campos

    (Ribeirão Preto Medical School- University of São Paulo)

  • Guilherme V. Polanczyk

    (Universidade de São Paulo)

  • Curtis Huttenhower

    (Harvard T.H. Chan School of Public Health)

  • Kirsten A. Donald

    (University of Cape Town)

  • Vanja Klepac-Ceraj

    (Wellesley College)

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.

Suggested Citation

  • Guilherme Fahur Bottino & Kevin S. Bonham & Fadheela Patel & Shelley McCann & Michal Zieff & Nathalia Naspolini & Daniel Ho & Theo Portlock & Raphaela Joos & Firas S. Midani & Paulo Schüroff & Anubhav, 2025. "Early life microbial succession in the gut follows common patterns in humans across the globe," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56072-w
    DOI: 10.1038/s41467-025-56072-w
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