Experimental design. Daphnia magna isoclonal lines were obtained from four distinct genotypes; three of these genotypes were revived from dormant embryos LRV3.5_15, LRV13.5_1, and LRV13.2, whereas P-IT is a reference laboratory genotype. For each genotype, germ-free and wild-type clonal populations were obtained. Germ-free clonal populations were obtained by exposing wild-type clonal replicates of the four genotypes to a cocktail of antibiotics (20 mg/L of tetracycline, streptomycin, and ampicillin). Both wild-type and germ-free lines were exposed in triplicated to glyphosate, Roundup, and control conditions (non-stress) after at least two generations in standard laboratory conditions to reduce interference from maternal effect. For each biological replicate, genotype, and treatment, genotoxicity via the comet assay, gut microbiota composition, fitness, and whole-genome transcriptional profiles were measured.