Gut microbiome of toddlers up to 36 months of age
Background: The infant gut microbiome undergoes rapid diet- and environment-driven maturation in early life. Characterisation of its taxonomic and functional profiles enables insight into microbial adaptation during this critical developmental period. This study aimed to characterise longitudinal gut microbiome dynamics and evaluate associations between taxonomic and functional composition and environmental exposures.  Results: A total of 108 faecal samples from 36 children across three time points (0-6, 6-12, and 12-36 months) were analysed using whole metagenome shotgun sequencing. The gut microbiome showed marked age-dependent shifts in taxonomic composition, with early dominance of Bifidobacteriaceae and Enterobacteriaceae transitioning to Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae at later stages. Alpha diversity increased significantly with age (Shannon index: 1.94 ± 0.63 to 3.96 ± 0.59, p < 0.05), while beta diversity demonstrated progressive convergence and stabilisation of microbial communities. Differential analysis identified 35 species varying across time points, with the majority enriched in the 12–36-month group. Age group was the primary driver of taxonomic variation (RDA, p = 0.005), followed by dietary and environmental factors. Functional profiling revealed age-associated shifts in metabolic and transport-related functions. While alpha diversity of functional profile remained stable, beta diversity differed significantly between age groups (p < 0.05), indicating functional restructuring. Differential analysis revealed 47 gene products varying across time points, predominantly enriched in older children. Early-life antibiotic exposure showed strong associations with both taxonomic and functional profiles, particularly during the first months of life.  Conclusions: The taxonomic and functional composition of the infant gut microbiome is primarily driven by age, with additional contributions from dietary and environmental factors. Microbial communities undergo a transition from early life dominance of facultative taxa to increased abundance of Bacteroidaceae and other anaerobes, coinciding with increasing diversity and community stabilisation after 12 months of age. Functional maturation is characterized by restructuring of gene profiles without major changes in functional alpha diversity. Early life antibiotic exposure showed limited long-term associations at the taxonomic level but was linked to persistent differences in functional profiles. These findings highlight the dynamic nature of microbiome development and the potential for early-life exposures to influence functional trajectories.
Background: The infant gut microbiome undergoes rapid diet- and environment-driven maturation in early life. Characterisation of its taxonomic and functional profiles enables insight into microbial adaptation during this critical developmental period. This study aimed to characterise longitudinal gut microbiome dynamics and evaluate associations between taxonomic and functional composition and environmental exposures.  Results: A total of 108 faecal samples from 36 children across three time points (0-6, 6-12, and 12-36 months) were analysed using whole metagenome shotgun sequencing. The gut microbiome showed marked age-dependent shifts in taxonomic composition, with early dominance of Bifidobacteriaceae and Enterobacteriaceae transitioning to Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae at later stages. Alpha diversity increased significantly with age (Shannon index: 1.94 ± 0.63 to 3.96 ± 0.59, p < 0.05), while beta diversity demonstrated progressive convergence and stabilisation of microbial communities. Differential analysis identified 35 species varying across time points, with the majority enriched in the 12–36-month group. Age group was the primary driver of taxonomic variation (RDA, p = 0.005), followed by dietary and environmental factors. Functional profiling revealed age-associated shifts in metabolic and transport-related functions. While alpha diversity of functional profile remained stable, beta diversity differed significantly between age groups (p < 0.05), indicating functional restructuring. Differential analysis revealed 47 gene products varying across time points, predominantly enriched in older children. Early-life antibiotic exposure showed strong associations with both taxonomic and functional profiles, particularly during the first months of life.  Conclusions: The taxonomic and functional composition of the infant gut microbiome is primarily driven by age, with additional contributions from dietary and environmental factors. Microbial communities undergo a transition from early life dominance of facultative taxa to increased abundance of Bacteroidaceae and other anaerobes, coinciding with increasing diversity and community stabilisation after 12 months of age. Functional maturation is characterized by restructuring of gene profiles without major changes in functional alpha diversity. Early life antibiotic exposure showed limited long-term associations at the taxonomic level but was linked to persistent differences in functional profiles. These findings highlight the dynamic nature of microbiome development and the potential for early-life exposures to influence functional trajectories.