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Using multiomics, pathway enrichment, and robust regression, we identified maternal anthropometrics and clinical indicators as key predictors of infant development, and specific metabolic and chemical exposures as major factors associated with microbiota composition. These microbial changes were associated with infant growth, eczema, and neurodevelopment. Notably, maternal metabolites (e.g., cholesterol) and environmental chemicals (e.g., triphenyl phosphate and perfluorobutane sulfonic acid) were associated with microbiota composition, particularly in Firmicutes, Proteobacteria, and Bacteroidetes. 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