Microscopic colitis (MC) is a disorder characterized by chronic non-bloody diarrhea predominantly affecting elderly smoking women. Since an altered microbiota is reported in several immune mediated diseases and since MC affects the gut, our hypothesis was that the microbiota would be altered in patients with MC. The bacterial microbiomes was analysed by DNA sequencing (Illumina Hiseq2000). Patients with MC had a marked reduction of Veruccomicrobia (Akkermansia spp) compared to healthy individuals. Specific Akkermansia spp PCR performed on the 10 patients and 7 controls and on an additional 5 female MC-patients confirmed the decreased levels of Akkermansia in MC patients.