Early-life maternal probiotic supplementation programs sex- and region–specific gene expression in the adult offspring brain

The maternal perinatal environment shapes brain development and long-term neurodevelopmental trajectories. Probiotic supplementation during this period has emerged as a promising strategy to support healthy neurodevelopmental outcomes through modulation of immune and synaptic plasticity pathways. However, the persistence and specificity of molecular effects in the offspring brain, particularly with respect to sex and brain region, remain poorly understood. We conducted two independent mouse experiments using different probiotic strains and exposure windows to evaluate the long-term transcriptional effects of maternal probiotic supplementation. Time-mated C57BL/6JRj dams received a multi-species probiotic (Ecologic® Panda) from gestational day (GD) 6 until birth, whereas BALB/cJRj dams received Limosilactobacillus reuteri ( L. reuteri ) from GD6 through postnatal day 7. The hippocampus and hypothalamus from adult male and female offspring were analyzed by RT-qPCR for genes related to synaptic plasticity, oxytocin signaling, neuroimmune regulation, myelination, and peptidoglycan (PGN) transport. Multi-species supplementation induced broad and persistent transcriptional changes in hippocampus and hypothalamus, with generally larger effects in males. Altered transcripts included markers of synaptic plasticity ( Bdnf , Ppp1r1b , Syp ), immune regulation ( Il10, Trem2 ), myelination ( Mag , Mog ), oxytocin signaling ( Oxtr ), and PGN transport ( Slc15a1 , Slc15a2 , Slc46a2 ). In contrast, L. reuteri produced selective, sex- and region-dependent transcriptional effects that differed by brain region and sex. Notably, across probiotic conditions, Il10 was consistently upregulated in both brain regions and sexes. These findings highlight that short, targeted maternal probiotic supplementation during the perinatal period is associated with persistent molecular signatures in the adult offspring brain across genetic backgrounds, converging on neuroimmune-related pathways. • Early-life maternal probiotics program persistent brain gene expression in adult offspring • Maternal probiotics induce distinct hippocampal and hypothalamic transcriptional profiles • Multi-species probiotics exert broader transcriptional effects than Limosilactobacillus reuteri • Sex-specific responses reveal differential brain sensitivity in males and females