Microbiota modulates compound-specific toxicity of environmental chemicals: A multi-omics analysis in zebrafish embryos

Interactions between gut microbiota and environmental chemicals critically influence toxicological outcomes, yet mechanistic insights remain limited. Here, we combine developmental toxicity with full-length 16S rRNA gene sequencing, transcriptomic, and metabolomic analyses in germ-free (GF) and conventionally colonized wild-type (WT) zebrafish embryos to elucidate the microbiota’s role in modulating chemical toxicity. Using representative compounds from major classes of environmental contaminants, we show that microbial presence significantly alters toxicity profiles in a compound-specific manner. The perfluorinated contaminant PFOS (perfluorooctanesulfonic acid) induced the strongest microbiota-dependent effects, with a greater number of differentially expressed genes in WT embryos and pronounced changes in immune and stress-related pathways. The pesticide boscalid and bisphenol F elicited distinct microbiota-modulated transcriptional and metabolic responses. Gene network analysis identified baseline microbial regulation of immune and metabolic programs, while metabolomics showed PFOS-dependent changes in L-tryptophan and its microbe-associated metabolites, including inosine, indoxyl sulfate and indole acetaldehyde, exclusively in WT embryos. These findings establish a mechanistically grounded framework for microbiota–chemical interactions and highlight the importance of integrating microbiome context into environmental health assessments.