Age-dependent patterns of gut Bifidobacterium microbiome in child cohort across a multi-ethnic population, Western China

The gut microbiome evolves dynamically throughout human development, influencing health at different life stages. However, current studies have primarily focused on infant and adult cohorts, leaving biomarkers associated with children in transitional developmental stages insufficiently explored, particularly in underrepresented regions and ethnic groups. Here, we profiled fecal microbiomes from 776 children (0–15 years) in the Ili Prefecture (Western China) using dual amplicon approaches: bacterial 16S rRNA V1-V3 amplicon sequencing and Bifidobacterium targeted groEL amplicon sequencing. First, groEL profiling improved taxonomic resolution for Bifidobacterium , identifying 22 (sub)species versus 11 with 16S, reducing the unclassified fraction (5.69% vs. 28.86%), and recovering low relative abundance taxa missed by 16S. Second, a Bayesian zero-inflated negative binomial (ZINB) analysis identified 4,047 age-related and 1,349 BMI-associated ZOTUs, and taxa with closer phylogenetic relationships exhibited more similar effect sizes; B. breve , B. pseudocatenulatum , and B. longum decreased with age, whereas B. adolescentis and B. faecale increased. Finally, cross-cohort comparisons replicated species-specific enrichments (e.g., B. longum subsp. infantis in Han; B. mongoliense in Mongolian populations) and indicated later bifidobacterial stabilization in the Ili cohort (~ 6 years) compared with the external cohort (~ 4 years), while Deming regression uncovered substantial consistency in age effect sizes between the Kazakh and Uyghur ethnic groups (β Deming = 1.12, 95% CI: [0.95, 1.30]). Taken together, this study provides new insights into the distinct, dynamic developmental trajectories of the bifidobacterial community in children across diverse populations.