The full impact of Alzheimer’s disease (AD) on the health of individuals is not yet fully understood. The characteristics of the gut microbiome in AD patients may provide hints for early detection and diagnosis of this disease. Research has investigated the ability of the 16S rRNA gene sequencing method to identify and interpret AD bacterial profiles. To identify specific bacteria involved in AD following the injection of amyloid beta and Donepezil, a metataxonomic technique was used. In this work, publicly available data were used to explore the composition of the fecal microbiota population in AD model mice and to determine the effects of the injection of amyloid beta and Donepezil. The protocol was conducted on 18 mice in the control group (n = 6), beta amyloid (Aβ) injection group (n = 6) and Donepezil-treated AD model group (n = 6). While Aβ led to cognitive dysfunction, drug treatment led to successful recovery from memory problems. The bacterial community profiling of AD mice was accomplished via 16S rRNA amplicon sequencing and the EzBiocloud pipeline. Our research revealed that the Aβ + Donepezil group presented significantly greater relative abundances of the Bacteroides and Akkermansia genera. The relative abundance of Akkermansia muciniphila in the Aβ + donepezil group was noted. These findings imply that the gut‒brain axis may play a role in the onset and amelioration of the cognitive impairment caused by Aβ. This study may provide fundamental information about how Donepezil and Aβ affect the gut microbiota in a mouse model of induced cognitive impairment, which could lead to new diagnostic and therapeutic strategies.