Establishing Life’s First Microbiome: Drivers, Modulators, and Dynamics of Infant Gut Colonization

The infant gut microbiome is a dynamic ecosystem whose assembly begins around birth and influences immune, metabolic, and developmental processes. Early colonization proceeds through ecological transitions from relatively low-diversity pioneer communities to increasingly complex and functionally mature ecosystems. This process is shaped by maternal microbial transmission, delivery mode, feeding, gestational age, host development, and environmental exposure. Although many studies have described associations between early-life microbiome composition and later health, important questions remain about how founding communities are established, which factors determine their succession, and how microbial priority effects influence subsequent ecosystem development. Recent longitudinal, strain-resolved, and multi-omic studies have improved understanding of maternal-to-infant transmission, functional maturation, and the role of human milk oligosaccharides and other ecological modulators. However, findings remain heterogeneous because of differences in sampling, cohort characteristics, analytical methods, and definitions of colonization. Further mechanistic and longitudinal investigation is needed to identify the ecological rules and biological drivers that govern infant gut microbiome assembly across diverse developmental and environmental contexts.This Research Topic aims to clarify the drivers, modulators, and temporal dynamics of initial gut microbiome colonization in infants. It will address how maternal, host, environmental, and nutritional factors influence the acquisition, persistence, succession, and functional development of early microbial communities. Contributions may examine hypotheses concerning vertical transmission, priority effects, niche construction, colonization resistance, and interactions between microbial colonization and immune or mucosal maturation. Studies using human cohorts and relevant animal models are encouraged, particularly those that integrate longitudinal sampling, strain-level resolution, multi-omic profiling, and mechanistic experimentation. The Research Topic will focus on foundational colonization biology rather than clinical interventions or long-term disease outcomes, thereby complementing Research Topics dedicated to therapeutic strategies targeting the early-life gut microbiota.To gather further insights into the establishment and development of the infant gut microbiome, this Research Topic will cover human and relevant animal model studies of early-life colonization, with emphasis on longitudinal, ecological, mechanistic, and methodologically rigorous research. We welcome original research, reviews, systematic reviews, perspective and all type of articles accepted by the journal addressing, but not limited to, the following themes:• Maternal-to-infant microbial transmission through vaginal, skin, oral, and breast milk microbiota• Vertical seeding routes and strain-level tracking of transmitted microorganisms• Effects of delivery mode, including vaginal birth and cesarean delivery, on early colonizers• Breastfeeding, formula feeding, and human milk oligosaccharides as ecological modulators• Gestational age, birth weight, prematurity, and other perinatal determinants of colonization trajectories• Environmental and household exposures, including siblings, pets, geography, and urban–rural differences• Microbial succession and ecological principles such as priority effects, niche construction, and colonization resistance• Host–microbe interactions involving immune maturation, genetics, epithelial development, and mucosal physiology• Multi-omic approaches, including metagenomics, metatranscriptomics, metabolomics, and proteomics• Longitudinal, strain-resolved, and spatial approaches for characterizing colonization dynamics• Methodological and technical considerations in sampling, sequencing, contamination control, and modeling early-life microbiome trajectories• Comparative studies linking infant gut colonization with relevant animal models Topic editors: Yaqin Wang, Fabricio Luiz Tulini, Ke Chen, Peilin Chen, Iyabo Christianah Oladipo Source: https://www.frontiersin.org/research-topics/85262/establishing-lifes-first-microbiome-drivers-modulators-and-dynamics-of-infant-gut-colonization