Exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome.

UNLABELLED: The exposome encompasses all lifetime environmental exposures affecting health. Its complexity and high data dimensionality make it challenging to link specific exposure combinations to adverse health outcomes. Establishing relevant exposome criteria is key to addressing current knowledge gaps. This study evaluated contaminant levels in Wisconsin groundwater and their effects on host health. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards: nitrate, atrazine, and imidacloprid, and the emerging contaminant, microplastics. In this study, broilers were exposed to a low-dose chemical mixture (35,000 ppb nitrate + 1.7 ppb atrazine + 0.58 ppb imidacloprid) and high-dose chemical mixture (100,000 ppb nitrate + 3,000 ppb atrazine + 3,000 ppb imidacloprid) or polyethylene microplastics (PE MPs) for 49 days. Both contaminant types significantly altered the cecal microbiomes as determined by the enrichment of the genera Fournierella and Ruminococcus and an unclassified Coriobacteriaceae genus. Untargeted metabolomics revealed distinct but convergent patterns of metabolic reprogramming across exposures. Chemical mixtures modulated pathways linked to xenobiotic metabolism, pyruvate and thiamine metabolism, and other cofactor-dependent processes, consistent with a shift from oxidative, biosynthetically intensive metabolism toward glycolysis, fermentation, and detoxification. In contrast, PE fibers selectively suppressed oxidative and cofactor/vitamin pathways while perturbing bile acid, sphingolipid, and aromatic compound metabolism, indicating a simplified, maintenance-oriented energy state. Despite these pronounced metabolomic shifts, histopathology revealed no overt intestinal or systemic lesions in any treatment group, highlighting altered microbial activity despite the absence of gross pathological lesions and supporting a silent dysbiosis phenotype.

IMPORTANCE: Environmental contaminants in groundwater are increasingly common, yet their combined effects on animal health remain poorly understood. The current study shows that even low-level exposure to agricultural chemical mixtures and microplastics can alter the gut microbial metabolism in broiler chickens without intestinal damage. These subclinical shifts, characterized by altered energy pathways, cofactor scarcity, and microbial restructuring, highlight a form of silent dysbiosis. Our findings emphasize the need to integrate microbiome- metabolic endpoints into environmental risk assessments to predict earlier, more meaningful, functionally relevant impacts.