Five Key Lessons from the CHAMP Study: Childhood Microbiome Health Across Pakistani Populations

The Childhood Health and Microbiome Programme (CHAMP) has been one of our most comprehensive research endeavours to date, enrolling over 300 children across three sites in KPK. Here we share five findings that have shaped how we think about childhood microbiome health in Pakistan.

1. Rural-urban differences are stark. Children from rural communities showed markedly different gut microbiome compositions compared to urban Peshawar children of the same age. Rural children had higher overall microbial diversity — a pattern that held even after adjusting for diet and breastfeeding practices — suggesting environmental exposure and reduced antibiotic use play important roles in early microbiome formation.

2. Breastfeeding duration predicts Bifidobacterium abundance. Among our CHAMP infants, every additional month of exclusive breastfeeding was associated with higher relative abundance of Bifidobacterium species at 12 months of age. This protective effect persisted even after complementary feeding was introduced, underscoring the lasting value of prolonged breastfeeding in shaping healthy infant microbiomes.

3. Antibiotic use leaves a detectable signature. Children who received three or more antibiotic courses in the first year of life showed significantly reduced microbial richness and lower counts of Lachnospiraceae family members at 18 months. Encouragingly, children who had a longer antibiotic-free period after their last course showed partial recovery, suggesting the microbiome has meaningful resilience.

4. Microbiome diversity at 6 months predicts weight-for-age at 18 months. One of our most striking longitudinal findings is that gut microbial diversity at 6 months — before growth divergence becomes obvious — is predictive of weight-for-age Z-score at 18 months. This positions early microbiome assessment as a potential screening tool to identify children at risk of future growth faltering.

5. The maternal microbiome matters. Stool microbiome profiles from mothers at delivery were moderately correlated with their infants' gut microbiome at 3 months, even after caesarean births. This suggests maternal-to-infant microbial transmission occurs through multiple routes and that maternal microbiome health during pregnancy should be considered part of any early-life nutrition intervention programme.