Gene-resolved deep metagenomics links impaired bile acid conversion and expanded p-cresol biosynthetic potential to a dominant commensal-to-pathobiont axis in a mouse model of antibiotic-induced Clostridioides difficile infection

This record contains the raw analytical data supporting the study of antibiotic-induced Clostridioides difficile infection in a mouse cecal model. The files provide three complementary metabolite datasets measured in cecal samples from Control, antibiotic-treated (Abx), and C. difficile-infected (Cdiff) mice: an untargeted LC-MS/MS metabolome, a targeted bile acid panel, and a targeted panel of p-cresol and its conjugates.