Up to 10% of women take selective serotonin reuptake inhibitor (SSRI) antidepressants during and after pregnancy to manage mood disorders, with possible implications for the developing offspring. The microbiota within the gastrointestinal tract contributes to the regulation of serotonin synthesis. However, the interaction between maternal depression, SSRI use, bacterial community composition, and availability of microbiota-derived metabolites during pregnancy and lactation is not clear, and may be consequential to the long-term health of mother and offspring. Therefore, to determine the impact of SSRI treatment on maternal microbial community dynamics, we conducted these studies in a rat model of maternal vulnerability (MV). All MV females have a genetic vulnerability, but only the ones exposed to early life stress in the form of maternal separation (MS) develop a depressive-like phenotype. In adulthood, MS- and control MV females were treated with either the SSRI fluoxetine (FLX) or the vehicle alone throughout pregnancy and lactation. High-resolution 16S ribosomal RNA marker gene sequencing and targeted metabolomic analysis were used to assess the fecal microbiome and metabolite availability, respectively.