SRP325707 PRJNA741672 GSE178956 HOST MICROBIOTA REGULATE SELECTIVE MYELOID SUBSETS IN THE CENTRAL NERVOUS SYSTEM DURING HOMEOSTASIS AND DISEASE The immune cells of the central nervous system (CNS) comprise parenchymal microglia and at the CNS border regions meningeal, perivascular and choroid plexus macrophages (summarized as CNS-associated macrophages, CAMs). Previous work has uncovered that microglial properties are strongly dependent on environmental signals from the commensal microbiota while its effect on CAMs remained unknown. By combining several microbiota manipulation approaches, genetic mouse models and single-cell RNA-sequencing, we comprehensively characterized CNS myeloid cell composition and function. Under steady-state, the transcriptional profile and numbers of choroid plexus macrophages were found to be tightly steered by complex microbiota. Divergently, perivascular and meningeal macrophages were affected to a lesser extent. An acute perturbation through viral infection evoked an attenuated immune response of all CAMs in germ-free mice. Additionally, we assessed CAMs in a more chronic pathological state in 5xFAD mice as a model for Alzheimer's disease whereby exclusively perivascular macrophages displayed enhanced amyloid beta uptake in GF 5xFAD mice. Our results provide novel insights for understanding distinct microbiota-CNS macrophage interactions during health and perturbation that could potentially be targeted therapeutically. Overall design: CNS-associated macrophages (CAMs) from the parenchyma, leptomeninges and choroid plexus were compared between mice housed in germ-free and controls housed in specific pathogen free conditions. Tissues from n = 5 mice per group were pooled for higher cell yields of CAMs. The different CNS compartments were separated, and myeloid cells were isolated as previously described with minor modifications (Erny et al., 2015, Jordao et al., 2019). GSE178956