Year: 2025
Type: review
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. Here, the authors provide a critical view of historical approaches to categorize microbial transmission in early life, and present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when.
Source: Nature Communications
Institutions: Broad Institute, Boston Children's Hospital, Harvard University, Johns Hopkins University, Universitat Pompeu Fabra, University of Trento, University of Oslo, Consejo Superior de Investigaciones Científicas, Universitat de València, Instituto de Agroquímica y Tecnología de Alimentos, University Medical Center Groningen, University of Groningen, University of Antwerp, Karolinska Institutet, UiT The Arctic University of Norway
Language: English
Topic: Gut microbiota and health
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funders: Universitetet i Tromsø, “la Caixa” Foundation, Ministerio de Ciencia, Innovación y Universidades, European Commission, ZonMw, Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Ministerio de Ciencia e Innovación, Utdannings- og forskningsdepartementet, National Institutes of Health, HORIZON EUROPE Framework Programme, Agencia Estatal de Investigación, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, Center for Advanced Study, University of Illinois at Urbana-Champaign, Ministerio de Universidades
Awards: G1255325603, G1338988596, G1855990336, G2099925525, G2262748287, G2660406951, G3480869486, G3518538256, G3681454997, G4042783231, G425668148, G434337789, G4857567810, G4944594896, G4993383890, G5099673792, G5178665745, G5362750019, G5421974903, G5497035506, G5635532810, G6004110409, Exposome-NL, G6314331178, Leveraging glycan-metabolite interactions to shape structure and function of the gut microbiome, G7084143925, G7863371703, G8497050386, G8920660035, Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiome, Immunological and Microbial Mechanisms in Food Allergy, Targeting microbial dysbiosis in Food Allergy to restore tolerance, Factors driving mother-to-infant microbiota transfer, Positive Selection as a Host Mechanism to Control the Microbiome
OpenAlex ID: W4413139359