PROJECT ABSTRACT/SUMMARY Alzheimer’s disease (AD) affects 5.5 million Americans and recent studies suggest that AD pathogenesis can be affected by the gut microbiota. We submit an extensively revised proposal in which we have identified three major mechanisms by which gut microbes may regulate AD: (i) APP processing and tau phosphorylation, (ii) modulating microglia, and (iii) activating peripheral immunity. We found that Bacteroides was linked to high levels of Aβ and Allobaculum was linked to low levels of Aβ, and we also identified metagenomic functions associated with Aβ. To find novel microbial mediators we will perform metabolomics. Administering Allobaculum reverses age-related changes in inflammatory expression in the cortex of WT mice and reversed markers of the microglia neurodegenerative disease phenotype (MGnD). In new preliminary data, we found that administering Bacteroides fragilis increased Aβ plaques and depleting Bacteroidetes with metronidazole decreased Aβ plaques. Both manipulations altered APP processing gene expression, including APP phosphorylation, trafficking from the golgi, and degradation by insulin degrading enzyme, which is a new potential microbially- driven mechanism that we will investigate in Aim 1. Of note, Bacteroides is increased in aging and AD in humans. Both microglia and peripheral monocytes play an important role in AD. In new preliminary data, we now show that colonizing mice with microbiota from AD patients increases Trem2 expression on microglia, which is a regulator of the MGnD phenotype, and that it decreases the expression of CCR2 on peripheral monocytes. CCR2+ monocytes traffic to the brain and are critical for the clearance of Aβ. Thus, we provide evidence that the AD microbiota can contribute to dysfunction in immune signaling pathways known to impact AD. We also show that administering specific bacteria or antibiotics modulates peripheral and central innate immunity. AIM 1: Which microbial factors alter AD pathogenesis in Aβ and tau animal models? We will determine whether (i) specific bacteria, (ii) individual antibiotics, and (iii) microbiota from AD subjects affect Aβ and tau pathology and cognitive decline. We will investigate whether this is linked with altered APP processing, regulation of Aβ degradation enzymes, activation of pro-amyloidogenic pathways, or with altering Tau phosphorylation. We will use 16S rRNA and shotgun metagenomic sequencing to identify bacteria and functions linked with AD pathology, and identify metabolites altered in models of AD. AIM 2: How does the microbiota modulate innate immunity in Aβ and tau animal models? We will investigate how microbiota interventions alter microglial migration and Aβ phagocytosis, and whether the microbiota modulate the switch between homeostatic and neurodegenerative microglia. We will test whether the microbiota alter monocyte migration to the brain and subsequent Aβ phagocytosis. We will establish whether microbial cell wall comp...