The apolipoprotein E4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), associated with early brain metabolic dysfunction and gut microbiome alterations. Targeting these early changes through dietary interventions may reduce AD risk in asymptomatic carriers. This study evaluated whether a ketogenic diet (KD) could reshape the gut microbiome and enhance key brain metabolite levels in young APOE4 mice, using APOE3 mice as a neutral-risk comparison. Male and female APOE3 and APOE4 mice were fed either a control diet or KD for 16 weeks, starting at 12 weeks of age. We used shotgun metagenomics and targeted brain metabolomics to identify microbe-metabolite signatures linked to neuroprotection. KD increased beneficial species such as Lactobacillus johnsonii and Lactobacillus reuteri while reducing pathogenic Bacteroides intestinalis. These microbial shifts correlated with improved brain metabolites related to mitochondrial function, neurotransmitter balance, redox homeostasis, and lipid metabolism. Notably, Lactobacillus species and B. intestinalis exhibited inverse correlations with key brain metabolite levels, suggesting their roles as both modulators and biomarkers of brain health. APOE4 females showed the greatest benefits, including restored microbiome diversity and normalization of brain metabolite levels. In contrast, APOE3 mice showed microbiome changes but limited brain metabolic responses. These findings highlight KD's potential to reprogram the gut-brain axis in a genotype- and sex-dependent manner, supporting its use as a precision nutrition strategy to reduce AD risk, particularly in asymptomatic female APOE4 carriers.
