Patients with Alzheimer’s disease (AD) have altered intestinal microbiota. Studies have shown that reduced intestinal microbiota in AD animal models decreases amyloid-beta (Aβ) plaque deposition. This age-related changes in the microbiota contribute to immunologic and physiologic decline. Previous study indicated that calorie restriction (CR) reduced brain Aβ deposition in Tg2576 mouse model of AD. This study examined whether CR alters the microbiome during aging. Mice were randomized to either an ad libitum (AL) or CR diet and they were singly housed in order to ensure that the appropriate number of calories were consumed. For every 1 g consumed by an AL-fed animal, 0.71 g of the CR diet was administered to the CR cohort. The dataset contains sequencing data. The data revealed that long-term CR may alter the gut environment and prevent the expansion of microbes that contribute to age-related cognitive decline.