Background: Currently, a specific diagnostic test for Alzheimer’s disease (AD) is not available. AD diagnosis is a long process that requires the execution of various clinical and instrumental tests. To date, the possibility of prevention, early diagnosis with prompt management of patients is almost impossible. Although CSF is considered the ideal sample for the evaluation of biomarkers of AD its collection is invasive, poorly tolerated by patients and expensive. Consequently, research is currently committed to identifying new biomarkers in easier-to-obtain biological samples such as blood and saliva. Recent knowledge highlights the role of the intestinal microbiota in neurodegenerative diseases (microbiota-gut-brain axis). Our hypothesis based on interplay between gut and brain is that microbiota alteration could influence stool composition, so our interest is focused on the fecal sample to identify biomarkers of AD. Objectives: The aim of the project is to identify diagnostic and prognostic biomarkers for AD using a multiomics approach (proteome and miRnome) on fecal samples Methods: The study was conducted on a transgenic mouse model of AD (3×Tg-AD) with three mutations associated with familial AD (APP-Swedish, MAPT-P301L, and PSEN1-M146V). miRNome and Proteomic analysis were performed by Next Generation Sequencing (NGS) and high definition mass spectrometry techniques, respectively. Results and conclusion: By Omics analyses we identified 31 microRNAs and 81 proteins differentially modulated in fecal samples from mutant mice with AD compared to wt controls, these molecules are potential biomarkers for AD. Their validation by Real-Time PCR, ELISA or immunoblotting is in progress. By this study, we demonstrated that the fecal sample is suitable to identify new biomarkes, also in neurodegenerative diseases. Furthermore, the use of the fecal sample implies multiple advantages, their collection is non-invasive and repeatable over time.