BACKGROUND Over the past two decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-lab procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis. OBJECTIVE In order to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population, « Le French Gut – Le microbiote français » aims to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata. METHODS “Le French Gut – Le microbiote français” is a prospective, non-interventional French national study involving individuals , the creation of a biological collection (feces) and the exploitation of data from questionnaires and the National Health Data System (SNDS, Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health, lifestyle, and dietary habits, and in which stool samples are self-collected. RESULTS Recruitment has started in September 2022 and is still on going. As of July 2024, we enrolled 14160 participants. CONCLUSIONS “Le French Gut” will provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host and diet. It aims to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine. CLINICALTRIAL ClinicalTrials.gov NCT05758961. Registered on 8 March 2023. The trial was prospectively registered.