Introduction: Acute ischemic stroke (AIS) is increasingly recognized as a systemic disorder in which gut microbiota dysbiosis drives neuroinflammation via the brain–gut axis. Akkermansia muciniphila (AKK), a commensal bacterium comprising ~3% of the human gut microbiota, has been linked to improved neurological recovery; however, its molecular mechanisms is unknown. We investigated how AKK modulates microglial lipid metabolism, signaling pathways, and inflammatory phenotypes after AIS. Methods: Male mice underwent permanent middle cerebral artery occlusion (pMCAO) and received AKK or vehicle. Neurological outcomes were assessed by Rotarod and Foot Fault tests. Single-cell RNA sequencing (scRNA-seq) profiled brain immune cell heterogeneity. Microglial phenotypes and lipid accumulation were evaluated by immunofluorescence, immunohistochemistry, and BODIPY staining. RT-qPCR quantified pro-inflammatory cytokines, and Western blot measured PSAP, GPR37, GPR37L, and p-ERK. Untargeted plasma metabolomics with KEGG pathway analysis identified AKK-modulated metabolites and lipid pathways. Results: scRNA-seq identified microglia as the principal AIS-affected cell type responsive to AKK, comprising four subclusters: disease-associated microglia (DAM), H-microglia (homeostatic), ATM (tissue-resident macrophage–like), and foam cells. In AKK-treated mice, 73 genes were upregulated and 27 downregulated in microglia, with enrichment of lipid transport/metabolism (Apoe, Apoc4) and “Lipid and atherosclerosis” plus NF-κB/TNF signaling pathways. pMCAO markedly increased foam cell–like microglia and lipid accumulation; AKK reduced these cells, restored PSAP/GPR37/ERK signaling, decreased total Iba1+ microglia, and enhanced M2 polarization (↑lba1+/CD206+). Metabolomics identified isorhamnetin as a key AKK-induced metabolite inversely correlated with neurological deficits. AKK restored beneficial sphingomyelins, improved glycerophospholipid/sphingolipid metabolism, reduced pro-inflammatory trimethylamine N-oxide, and enriched lysosome-related pathways. Conclusion: AKK confers neuroprotection after AIS by increasing isorhamnetin, activating PSAP/GPR37/ERK signaling, and reprogramming microglia from pro-inflammatory foam cells toward a reparative M2 phenotype, while restoring phospholipid homeostasis and reducing harmful microbial metabolites. This work defines a novel gut microbe–metabolite–signaling axis in AIS and highlights AKK as a promising, translational therapeutic strategy.
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