CHLORINATED drinking water exposure in infancy was linked to increased antimicrobial resistance pathways in the gut microbiome, according to a new Australian randomised controlled trial.
Chlorinated Water and Infant Gut Health
Water chlorination remains one of the most effective public health measures for preventing waterborne infectious diseases. However, researchers investigated whether prolonged exposure to chlorine-based disinfectants during infancy could also influence the developing gut microbiome, a critical factor in immune and metabolic health.
The waTer qUality and Microbiome Study enrolled 197 infants aged 6 months and randomly assigned them to receive either filtered de-chlorinated water or standard chlorinated tap water for 12 months. The double-blinded design aimed to assess whether chlorinated drinking water altered gut microbial composition or function during a key developmental window.
Gut Microbiome Diversity Remained Stable
Researchers collected stool and tap water samples at baseline and following the intervention period. Metagenomic sequencing showed that overall gut microbiome diversity remained broadly similar between groups.
There were no significant differences in beta diversity (0.56% variance explained; p=0.84), microbial richness (−4.25; 95% CI: −14.85–6.35; p=0.43), or Shannon diversity index (−0.14; 95% CI: −0.32–0.04; p=0.12) between infants exposed to chlorinated water and those receiving filtered water.
These findings suggested that chlorinated drinking water did not substantially disrupt the overall structure of the infant gut microbiome during the study period.
Antimicrobial Resistance Pathways Increased
Despite the stable microbial composition, infants exposed to chlorinated water showed enrichment of antimicrobial resistance-related MetaCyc pathways.
Researchers also found that this effect appeared stronger in infants who had received clinical antibiotics.
The findings suggest that chlorine-based disinfectants may create selective pressures favouring microbial resistance functions, even without major shifts in bacterial diversity.
Implications for Public Health
The researchers emphasised that water chlorination remains essential for preventing serious infectious disease outbreaks and protecting population health.
However, they noted that the findings highlighted the need for further investigation into how disinfected water may influence early-life microbial development.
Future studies may explore whether modifying the timing or delivery of disinfected drinking water during infancy could help reduce antimicrobial resistance pressures while maintaining water safety standards.
Reference
Parkin K et al. Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomised trial. Commun Med. 2026;DOI:10.1038/s43856-026-01626-2.
Featured image: Brian Jackson on Adobe Stock
