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Here, we investigated the role of microbiota in microglial activation during aGVHD using antibiotic-treated specific pathogen\u2013free (SPF), germ-free (GF), and wildling mice. Antibiotic-mediated microbiota depletion led to infiltration of IFN-\u03b3\u2013producing T cells in the brain, activation of microglia via the TLR4\/p38 MAPK pathway, and neurocognitive deficits in SPF aGVHD mice. Microglial depletion reversed the neurocognitive deficits. GF and wildling mice treated with antibiotics exhibited similar microglial activation after allogeneic hematopoietic cell transplantation (allo-HCT). Mechanistically, the bacteria-derived metabolite N,N,N-trimethyl-5-aminovaleric acid (TMAVA) was decreased in microglia following antibiotic treatment. TMAVA administration suppressed TLR4\/p38 MAPK pathway activity in microglia and alleviated gut microbiota depletion\u2013mediated neurocognitive deficits. 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