A reconceptualized framework for human microbiome transmission in early life

Mostra el registre complet Registre parcial de l'ítem

• dc.contributor.author Rakoff-Nahoum, Seth
• dc.contributor.author Debelius, Justine
• dc.contributor.author Vallès Colomer, Mireia
• dc.contributor.author Noordzij, Hanna Theodora
• dc.contributor.author Esteban-Torres, María
• dc.contributor.author Zhernakova, Alexandra
• dc.contributor.author Brusselaers, Nele
• dc.contributor.author Pettersen, Veronika Kuchařová
• dc.date.accessioned 2025-11-10T14:47:42Z
• dc.date.available 2025-11-10T14:47:42Z
• dc.date.issued 2025
• dc.date.updated 2025-11-10T14:47:42Z
• dc.description.abstract Human development and physiology are fundamentally linked with the microbiome. This is particularly true during early life, a critical period for microbiome assembly and its impact on the host. Understanding microbial acquisition in early life is thus central to both our basic understanding of the human microbiome and strategies for disease prevention and treatment. Here, we review the historical approaches to categorize microbial transmission originating from the fields of infectious disease epidemiology and evolutionary biology and discuss how this lexicon has influenced our approach to studying the early-life microbiome, often leading to confusion and misinterpretation. We then present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when. We present ways these parameters may be assigned, with a particular focus on the 'transmitted strain' through metagenomics to capture these elements. We end with a discussion of approaches for implementing this framework toward defining each component of microbiome acquisition.
• dc.description.sponsorship This project was possible through a grant awarded to V.K.P. by the Center for Advanced Study (CAS) in Oslo, Norway, which funded and hosted the Young CAS research project (Infant Gut Microbiome Acquisition: Off to a Healthy Start) during the 2022/23 academic year. CAS is an independent research foundation funded by the Norwegian Ministry of Education and Research. We also acknowledge and appreciate our partners and children who enabled and enlivened our discussions during the summer of 2023 in Tromsø, Norway. S.R.-N. acknowledges support from the Mathers Foundation, a Career Award for Medical Scientists from the Burroughs Wellcome Fund, a Pew Biomedical Scholarship, and National Institutes of Health (R01DK138023, R01AI158814, R01AI171100, R01AI126915). M.V.-C. acknowledges funding from the Spanish Ministry of Science and Innovation (Knowledge Generation Project PID2022-139328OA-I00), the Spanish Ministry of Universities (Beatriz Galindo Junior fellowship BG22/00172), and from La Caixa Foundation (Junior Leader fellowship 100010434, code LCF/BQ/PI24/12040001). M.E.T. acknowledges funding from the European Union's Horizon 2020 (MSCA-IF postdoctoral grant MicroMi-898088), and Ramón y Cajal grant RYC2023-045839-I, Ministry of Science, Innovation and Universities, the State Research Agency MCIU/AEI/10.13039/501100011033 and FSE+. The Institute of Agrochemistry and Food Technology (IATA-CSIC) is a Center of Excellence Severo Ochoa (CEX2021- 001189-S MCIN/AEI/10.13039/501100011033). A.Z. is supported by the Netherlands Organization for Scientific Research NWO-VICI grant VI.C.232.074, the NWO Gravitation grant Exposome-NL(024.004.017), the NWO KIC grant KICH1.LWV04.21.01, the ZonMW ME/CFS grant 10091012110015, EU Horizon Europe Program grant INITIALIZE (101094099), and EU Horizon Europe Program grant DarkMatter (ID-DarkMatter-NCD, 101136582).
• dc.format.mimetype application/pdf
• dc.identifier.citation Rakoff-Nahoum S, Debelius J, Valles-Colomer M, Noordzij HT, Esteban-Torres M, Zhernakova A, Brusselaers N, Pettersen VK. A reconceptualized framework for human microbiome transmission in early life. Nat Commun. 2025 Aug 14;16(1):7546. DOI: 10.1038/s41467-025-61998-2
• dc.identifier.doi http://dx.doi.org/10.1038/s41467-025-61998-2
• dc.identifier.issn 2041-1723
• dc.identifier.uri http://hdl.handle.net/10230/71835
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof Nature Communications. 2025;16(1):7546
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2022-139328OA-I00
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/898088
• dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101094099
• dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101136582
• dc.rights © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
• dc.subject.keyword Microbial ecology
• dc.subject.keyword Microbiome
• dc.title A reconceptualized framework for human microbiome transmission in early life
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion