Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice

Alzheimer's disease (AD) is a fatal neurodegenerative disease. APOE4 is the greatest genetic risk factor for AD, increasing risk up to 15-fold compared to the common APOE3. Importantly, female (?) APOE4 carriers have a greater risk for developing AD and an increased rate of cognitive decline compared to male (?) APOE4 carriers. While recent evidence demonstrates that AD, APOE genotype, and sex affect the gut microbiome (GM), how APOE genotype and sex interact to affect the GM in AD remains unknown.This study analyzes the GM of 4-month (4M) ? and ? E3FAD and E4FAD mice, transgenic mice that overexpress A?42 and express human APOE3 or APOE4. The microbial community structure of mouse feces was analyzed using high-throughput sequencing of 16S ribosomal RNA gene amplicons and clustering of data into operational taxonomic units (OTU). ?- and ?-diversity of the EFAD mice GM were compared across APOE, sex and stratified by sex and APOE, resulting in 4 cohorts (?E3FAD, ?E3FAD, ?E4FAD and ?E4FAD). Analysis of similarity was performed to determine if communities between groups were significantly different. Mann-Whitney tests under Monte Carlo simulation and machine-learning algorithms were used to identify significantly differentially abundant taxa associated with APOE and sex. Significant differences in the bacterial composition of young EFAD mouse GM were primarily associated with APOE genotype and to a much lesser extent sex. Stratification by sex and APOE revealed that ?E4FAD mice exhibit a GM significantly different from ?E3FAD mice, and ?E4FAD mice exhibit a GM significantly different from ?E3FAD mice. Six genus-level taxa were significantly differently abundant between APOE genotype and one taxon was significantly different abundant by sex. Stratification by genotype and sex revealed that the relative abundance of bacteria from the genera Prevotella and Ruminococcus was significantly higher in ?E4FAD mice relative to ?E3FAD mice, while the relative abundance of Sutterella was significantly higher in ?E4FAD mice relative to ?E3FAD mice. A machine-learning algorithm identified 29 OTUs contributing to differentiation of sample groups, and this analysis revealed significant clustering of ?E4FAD mice apart from all other animals.