Maternal microbiota shapes brain and neuroendocrine development in piglets

The maternal microbiota plays a critical role in early-life development, yet how maternal microbiota exposure shapes cellular and neuroendocrine programs during mammalian development remains poorly understood. Here, leveraging germ-free (GF) and maternal microbiota transplantation (MMT) models, we generated an integrated multi-organ porcine atlas by combining multi-regional single-nucleus RNA sequencing, spatial transcriptomics, bulk RNA sequencing of intestinal tissues, and metabolomics. Across five brain regions and the hypothalamic-pituitary-adrenal (HPA) axis, we profiled 673,623 high-quality nuclei and revealed microbiota-dependent remodeling of neuronal and glial states across early postnatal developmental stages. MMT reshaped neuronal maturation programs, altered the distribution of immature neuronal states, and elicited region-specific transcriptional responses in glutamatergic and GABAergic neurons. MMT also reorganized neuron-glia interaction networks, accompanied by trends toward increased plasma glutamic acid and glutamine levels. Across the gut-brain-neuroendocrine axis, MMT was associated with coordinated remodeling of HPA-axis cellular communication, stress-response transcriptional programs, and immune signatures, together with reduced circulating cortisol levels. Integrated intestinal analyses revealed segment-specific transcriptional and metabolic remodeling, including alterations in tryptophan/indole-related metabolites and immune-associated pathways. Cross-species stratified linkage disequilibrium score regression further identified enrichment of human cognitive and neuropsychiatric trait-associated genetic signals within cell-type-specific gene signatures derived from microbiota-responsive porcine cell populations. Our study establishes a large-animal cellular atlas linking maternal microbiota-responsive remodeling across the brain, gut, and neuroendocrine axis, providing a translational framework for understanding how early-life microbial signals shape mammalian developmental physiology.