We found that inulin had many similar beneficial effects in the gut and brain for both APOEε3 FAD (E3FAD) and APOEε4 FAD (E4FAD mice) and may be protective for brain functions and reduce risk of neurodegeneration.. E3FAD and E4FAD mice also had distinct responses in several metabolic pathways, suggesting an APOE-dependent nutrigenetic effect in modulating systemic metabolism and neuroprotection.