Alzheimer’s disease (AD) remains the most common form of dementia, affecting 50 million people worldwide. Recent studies from our laboratory established a clear role for the gut microbiome in the pathology of AD. These studies also suggested rampant neuroinflammation in the AD brain, triggered by imbalances in gut microbiome diversity. However, the exact mechanism through which the gut microbiome exerts its effect on the AD brain remains unknown. The present study aims to identify temporal changes in microglial gene expression after antibiotic treatment and fecal microbiome transplantation (FMT) on the progression of AD. We anticipate that these studies will provide new insights into the molecular mechanisms of gut-brain communication, which may lead to development of new therapeutic approaches for AD treatment.