Age-related changes in the urinary microbiome of healthy Japanese children

The human urinary tract, once considered sterile, is now known to harbor a complex microbial community termed the "urobiome." In adults, the urobiome is shaped by sex and hormonal changes, but its developmental trajectory in healthy children remains poorly defined. Establishing a pediatric baseline is essential for understanding how dysbiosis may contribute to conditions such as urinary tract infections or enuresis. This study provides a comprehensive analysis of the urobiome in a healthy Japanese pediatric cohort, contributing geographical and ethnic diversity to a field largely dominated by Western studies.

To characterize age- and sex-specific developmental changes in the urinary microbiome of healthy Japanese children and compare them with adults.

Midstream urine was collected from 93 healthy children (54 males; median age 7.0 years) and 60 adults (30 males; median age 22.9 years). Participants were stratified into four age groups: 3-5 years, 6-10 years, 11-15 years, and adults. Bacterial composition was analyzed via 16S rRNA gene sequencing (V3-V4). Alpha diversity (Shannon, Chao1) and beta diversity (Bray-Curtis dissimilarity, Principal Coordinate Analysis) were assessed.

In males, Shannon diversity was significantly higher in the 3-5-year-old group than in the 6-10 (p = 0.047) and 11-15-year-old (p = 0.0019) groups. In females, diversity differed significantly across all groups (p < 0.001), decreasing after puberty. Beta diversity analysis revealed a marked compositional shift around puberty in females and a distinct separation of adult males from pediatric groups (PERMANOVA, p = 0.001 for both). At the genus level, females showed a post-pubertal increase in Lactobacillus and Bifidobacterium. In males, Ezakiella and Prevotella decreased in adulthood, while Bifidobacterium became detectable and increased (all p < 0.05).

Our findings demonstrate a dynamic, multi-stage maturation of the pediatric urobiome. In females, the post-pubertal decline in alpha diversity, driven by Lactobacillus dominance, indicates transition to a more specialized, stable community. In males, the emergence of a distinct adult profile suggests a more gradual maturation process. A limitation is the cross-sectional design; longitudinal studies are required to confirm individual developmental trajectories.

The healthy pediatric urobiome undergoes distinct age- and sex-specific maturation, reaching adult-like profiles after puberty. These results establish a critical baseline for normal pediatric urobiome development and provide a foundation for identifying dysbiosis in pediatric urological and systemic diseases.