Abstract
Background: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.
Objective: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.
Design: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n = 197) received either de-chlorinated drinking water via benchtop filtration (treatment, n = 99), or regular chlorinated water (control, n = 98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.
Results: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p = 0.84), richness (−4.25, 95% CI; −14.85 to 6.35, p = 0.43) or Shannon Index (−0.14, 95% CI; −0.32 to 0.04, p = 0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p < 0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.
Conclusion: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.
Trial registration: ACTRN12619000458134; https://www.anzctr.org.au
Keywords
infant gut microbiome, drinking water chlorination, antimicrobial resistance, water quality, infant health, gut microbial ecology
Document Type
Journal Article
Date of Publication
12-1-2026
Article Number
405
E-ISSN
2730664X
Volume
6
Issue
1
Publication Title
Communications Medicine
Publisher
Nature
School
Nutrition and Health Innovation Research Institute / School of Medical and Health Sciences
RAS ID
99972
Funding Information
This research was funded by the Kids Research Institute Australia Bluesky award, and the Water Corporation WA. This study received partial funding from the Water Corporation WA to support the costs associated with home tap water analysis and metagenomic sequencing.
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Recommended Citation
Parkin, K., Christophersen, C. T., Verhasselt, V., Palmer, D. J., Cooper, M. N., Prescott, S. L., Silva, D., & Martino, D. (2026). Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: A randomized trial. Communications Medicine, 6. https://doi.org/10.1038/s43856-026-01626-2