Altered Gut Microbiota Mediates the Association between APOE Genotype and Amyloid-β Accumulation in Middle-Aged Adults

Abstract Importance The apolipoprotein E ( APOE ) ε4 allele is the strongest genetic risk factor for Alzheimer’s disease (AD), yet the mechanisms linking APOE to amyloid-β (Aβ) pathology remain incompletely understood. Emerging evidence suggests that the gut microbiome may modulate neurodegeneration; however, its role as a mediator in the APOE–Aβ relationship remains unclear. Objective To evaluate whether specific microbial taxa mediate APOE-related effects on brain Aβ burden in an established population-based study of middle-aged adults. Design, Setting, and Participants This cross-sectional study analyzed data from the Framingham Heart Study cohort. Data were collected at the third examination visit (n = 227, %Female = 58, mean age = 56.5 ± 8.3), between 2016 and 2019. Exposures Gut bacterial DNA was sequenced using 16S rRNA, and amplicon sequence variants (ASVs) were agglomerated at various taxonomic levels (14 phyla, 70 families, and ∼140 genera). APOE genotypes were derived from blood DNA using PCR and restriction isotyping. Predicted microbial functional potential was based on KEGG Orthologs. Main Outcomes and Measures Overall and regional measures of cerebral amyloid-β deposition were assessed using carbon-11 Pittsburgh (PiB) Compound-B PET scans. The global PiB deposition served as the primary outcome for “ overall ” amyloid burden. Regional amyloid deposition values were analyzed as secondary outcomes. Results A higher Aβ burden was significantly associated with the depletion of protective genera (e.g., Faecalibacterium β [95%CI],-0.35 [-0.40,-0.30]; Ruminococcus -0.25 [-0.27,-0.23]; Butyricicoccus -0.27 [-0.32,-0.22]) and the enrichment of pro-inflammatory taxa (e.g., Alistipes 0.07 [0.06, 0.08], Bacteroides 0.10 [0.07, 0.13]) and Barnesiella (0.18 [0.16, 0.20]). These associations were more pronounced in APOE ε4 carriers, who exhibited a broader spectrum of microbial dysbiosis. Mediation analysis showed that Ruminococcus , Butyricicoccus , Clostridium , and Christensenellaceae collectively mediated ∼0.3-0.4% of the effect of APOE ε4 on global Aβ burden. Functional profiling revealed a reduced abundance of microbial genes involved in key metabolic pathways among individuals with higher Aβ levels. Conclusion and Relevance Gut microbiome composition partially mediates the relationship between APOE ε4 and cerebral amyloid burden. These findings support a gut-brain axis mechanism in AD and suggest that microbiome-targeted interventions may mitigate APOE -related risk.