In an attempt to explore the microbial content of colonic crypts of the mouse gut that contain the stem cells, thereby accounting for epithelial regeneration, we proceeded to targeted molecular microbial diagnostic. We showed that only the caecal and colonic crypts harbor a living resident flora in the mouse. CSCM is unexpectedly dominated by strictly aerobic genus such as Acinetobacter, Delftia and Stenotrophomonas (Pédron T et al, mBio, 2012). We suggest that the CSCM plays both a protective and a homeostatic role in the crypt, thus severe consequences may result from its displacement by a more aggressive genus (i.e. pathobionts). We also analyse the impact of different diets in CSCM composition. Moreover we are currently characterizing the CSCM in human colonic crypts and its variations in pathological situations such as colon cancer (Team involved in PMM in these projects: Céline Mulet, Thierry Pédron, Azadeh Saffarian, Julie Tomas).