Data and figures are provided on the effects of fluoxetine, a selective serotin reuptake inhibitor (SSRI) antidepressant, on the gut microbiome and metabolome in a rat model to better understand the effect of this drug on women during gestation and lactation. Throughout pregnancy and lactation, female rats received the SSRI fluoxetine or vehicle. High resolution 16S ribosomal RNA marker gene sequencing and targeted metabolic analysis were used to assess the fecal microbiome and metabolic availability, respectively.