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

Ngouongo, Y. W.; Bernal, R.; NJAMNSHI, W. Y.; Satizabal, C. L.; Beiser, A.; Ruiz, A.; NJAMNSHI, A. K.; Vasan, R. S.; Seshadri, S.; Himali, J. J.; Fongang, B.

doi:10.1101/2025.07.27.667048

bioRxiv · 10.1101/2025.07.27.667048

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

Ngouongo, Y. W.·Bernal, R.·NJAMNSHI, W. Y.·Satizabal, C. L.·Beiser, A.·Ruiz, A.·NJAMNSHI, A. K.·Vasan, R. S.·Seshadri, S.·Himali, J. J.·Fongang, B.

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Abstract

ImportanceThe apolipoprotein E (APOE) {varepsilon}4 allele is the strongest genetic risk factor for Alzheimers disease (AD), yet the mechanisms linking APOE to amyloid-{beta} (A{beta}) pathology remain incompletely understood. Emerging evidence suggests that the gut microbiome may modulate neurodegeneration; however, its role as a mediator in the APOE-A{beta} relationship remains unclear. ObjectiveTo evaluate whether specific microbial taxa mediate APOE-related effects on brain A{beta} burden in an established population-based study of middle-aged adults. Design, Setting, and ParticipantsThis 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. ExposuresGut 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 MeasuresOverall and regional measures of cerebral amyloid-{beta} 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. ResultsA higher A{beta} burden was significantly associated with the depletion of protective genera (e.g., Faecalibacterium {beta} [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 {varepsilon}4 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 {varepsilon}4 on global A{beta} burden. Functional profiling revealed a reduced abundance of microbial genes involved in key metabolic pathways among individuals with higher A{beta} levels. Conclusion and RelevanceGut microbiome composition partially mediates the relationship between APOE {varepsilon}4 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.

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Ngouongo, Y. W., Bernal, R., NJAMNSHI, W. Y., Satizabal, C. L., Beiser, A., Ruiz, A., NJAMNSHI, A. K., Vasan, R. S., Seshadri, S., Himali, J. J., Fongang, B.. 2025-07-31. Altered Gut Microbiota Mediates the Association between APOE Genotype and Amyloid-β Accumulation in Middle-Aged Adults. https://doi.org/10.1101/2025.07.27.667048

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