Beneath The Surface: Uncovering Disruptions in the Human Microbiome as a Consequence of Drinking Chlorinated Water

Abstract

Chlorination of drinking water is a cornerstone of modern public health, yet its potential impact on the human gut microbiome remains poorly understood. This study investigates the relationship between drinking water source, used as a proxy for chlorination exposure, and microbiome composition across the United States using data from the Human Microbiome Compendium. State-level microbiome profiles were analyzed alongside census-derived estimates of reliance on domestic well water, with multivariate statistical approaches including principal component analysis (PCA), PERMANOVA, and multiple regression on matrices (MRM) used to assess associations while accounting for confounding variables. Microbiome composition differed significantly between states, and a statistically significant association was identified between microbiome structure and reliance on domestic well water. This relationship persisted after controlling for geographic, socioeconomic, and antibiotic usage factors. Further analyses indicated that the observed differences were not driven by individual taxa, but rather reflected a distributed, community-wide restructuring of the microbiome. Although certain genera, including Bacteroides, contributed strongly to overall variation, no single genus independently explained the observed patterns. These findings suggest that chlorination exposure may be a source of broad ecological pressure on the gut microbiome, potentially influencing microbial composition through mechanisms consistent with its known oxidative activity. However, interpretation is limited by dataset heterogeneity, incomplete geographic coverage, and the use of an indirect proxy for chlorination exposure. Overall, this study provides preliminary evidence that drinking water treatment practices may represent an underrecognized environmental factor shaping the human microbiome. Further controlled and longitudinal studies are needed to establish causality and to better understand the implications of chronic, low-level chlorine exposure for human health.