Infection-Specific Reprogramming of Microglia Reveals Distinct Virulence Pathways Linking Periodontal Pathogens to Alzheimer’s Disease

Microglial dysregulation is increasingly recognized as a driver of Alzheimer’s disease (AD), yet how pathogen-specific cues sculpt microglial diversity remains unclear. Here we integrate high-dimensional single-cell cytometry in vitro with spatial proteomics in vivo to dissect the impact of two major periodontal pathogens on microglia. Using a 36-marker CyTOF panel, we exposed SIM-A9 microglia to wild-type Porphyromonas gingivalis (Pg) or Tannerella forsythia (Tf) and to gingipain-deficient or S-layer–deficient mutants, resolving 38 clusters. Virulence-factor “switches” redirected cells from homeostatic states toward i) oxidative, antigen-presenting programmes driven by Pg gingipains and ii) an immunosuppressive, exhausted-like state driven by the Tf S-layer. Complementary 37-marker imaging mass cytometry of 5xFAD × hTau knock-in mice chronically infected with Pg identified 21 microglial subclusters. The cortex—but not hippocampus—lost two Arg1⁺/IL-10⁺ immunoregulatory subsets (>2-fold decrease) while NADPH-oxidase-high microglia accumulated around amyloid-β and tau aggregates. These data demonstrate pathogen-specific reprogramming of microglia across model systems and brain regions, linking virulence-factor activity to AD-relevant neuroinflammation. By pinpointing gingipains and the bacterial S-layer as molecular “switches,” our study highlights tractable therapeutic targets for limiting infection-driven microglial dysfunction in Alzheimer’s disease.