# Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation

## TL;DR

The biliary microbiome in children with choledochal cysts shows stable species composition but significant functional changes as children grow, with early childhood being a key period for microbial adaptation.

## Contribution

This study reveals age-dependent functional remodeling of the biliary microbiome in pediatric choledochal cyst patients despite taxonomic stability.

## Key findings

- The biliary microbiome's taxonomic composition and diversity remain stable across age groups in children with choledochal cysts.
- Early childhood (1–5 years) shows the highest number of unique functional genes and metabolic pathways in the biliary microbiome.
- Infants (<1 year) have the most unique antibiotic resistance and virulence genes, which decrease in older children.

## Abstract

Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1–5 years), and later childhood (5–12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1–5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of “taxonomic conservation coupled with functional remodeling” in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.