Early life microbial succession in the gut follows common patterns in humans across the globe
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...
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-56072-w |
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| author | 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 Das Inoli Shennon Brooke C. Wilson Justin M. O’Sullivan Robert A. Britton Deirdre M. Murray Mairead E. Kiely Carla R. Taddei Patrícia C. B. Beltrão-Braga Alline C. Campos Guilherme V. Polanczyk Curtis Huttenhower Kirsten A. Donald Vanja Klepac-Ceraj |
| author_facet | 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 Das Inoli Shennon Brooke C. Wilson Justin M. O’Sullivan Robert A. Britton Deirdre M. Murray Mairead E. Kiely Carla R. Taddei Patrícia C. B. Beltrão-Braga Alline C. Campos Guilherme V. Polanczyk Curtis Huttenhower Kirsten A. Donald Vanja Klepac-Ceraj |
| author_sort | Guilherme Fahur Bottino |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-1004f8ad6f1b4a408f48630c8ce0f801 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-1004f8ad6f1b4a408f48630c8ce0f8012025-01-19T12:30:45ZengNature PortfolioNature Communications2041-17232025-01-0116111210.1038/s41467-025-56072-wEarly life microbial succession in the gut follows common patterns in humans across the globeGuilherme Fahur Bottino0Kevin S. Bonham1Fadheela Patel2Shelley McCann3Michal Zieff4Nathalia Naspolini5Daniel Ho6Theo Portlock7Raphaela Joos8Firas S. Midani9Paulo Schüroff10Anubhav Das11Inoli Shennon12Brooke C. Wilson13Justin M. O’Sullivan14Robert A. Britton15Deirdre M. Murray16Mairead E. Kiely17Carla R. Taddei18Patrícia C. B. Beltrão-Braga19Alline C. Campos20Guilherme V. Polanczyk21Curtis Huttenhower22Kirsten A. Donald23Vanja Klepac-Ceraj24Department of Biological Sciences, Wellesley CollegeDepartment of Biological Sciences, Wellesley CollegeUniversity of Cape TownDepartment of Biological Sciences, Wellesley CollegeUniversity of Cape TownSchool of Arts, Sciences and Humanity, University of São PauloThe Liggins Institute, The University of AucklandThe Liggins Institute, The University of AucklandAPC Microbiome IrelandDepartment of Molecular Virology and Microbiology, Baylor College of MedicineSchool of Arts, Sciences and Humanity, University of São PauloAPC Microbiome IrelandThe Liggins Institute, The University of AucklandThe Liggins Institute, The University of AucklandThe Liggins Institute, The University of AucklandDepartment of Molecular Virology and Microbiology, Baylor College of MedicineINFANT Maternal and Child Health Centre, Dept of Paediatrics and Child Health, University College CorkINFANT Maternal and Child Health Centre, Dept of Paediatrics and Child Health, University College CorkMicrobiology Department, Institute of Biomedical Sciences (ICB-II), University of São PauloMicrobiology Department, Institute of Biomedical Sciences (ICB-II), University of São PauloPharmacology of Neuroplasticity Lab- Department of Pharmacology, Ribeirão Preto Medical School- University of São PauloDivision of Child & Adolescent Psychiatry, Department & Institute of Psychiatry, Faculdade de Medicina FMUSP, Universidade de São PauloDepartment of Biostatistics, Harvard T.H. Chan School of Public HealthUniversity of Cape TownDepartment of Biological Sciences, Wellesley CollegeAbstract 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.https://doi.org/10.1038/s41467-025-56072-w |
| spellingShingle | 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 Das Inoli Shennon Brooke C. Wilson Justin M. O’Sullivan Robert A. Britton Deirdre M. Murray Mairead E. Kiely Carla R. Taddei Patrícia C. B. Beltrão-Braga Alline C. Campos Guilherme V. Polanczyk Curtis Huttenhower Kirsten A. Donald Vanja Klepac-Ceraj Early life microbial succession in the gut follows common patterns in humans across the globe Nature Communications |
| title | Early life microbial succession in the gut follows common patterns in humans across the globe |
| title_full | Early life microbial succession in the gut follows common patterns in humans across the globe |
| title_fullStr | Early life microbial succession in the gut follows common patterns in humans across the globe |
| title_full_unstemmed | Early life microbial succession in the gut follows common patterns in humans across the globe |
| title_short | Early life microbial succession in the gut follows common patterns in humans across the globe |
| title_sort | early life microbial succession in the gut follows common patterns in humans across the globe |
| url | https://doi.org/10.1038/s41467-025-56072-w |
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