Inflammatory Bowel Diseases are associated with a disruption of the intestinal microbiota, called dysbiosis, determining event in the pathogenesis. Interactions between host and microbiota occur through various factors, including anti-microbial peptides. Recently, we and others have identified fecal miRNAs as new functional entities in the gut that could play a role on both microbiota and intestinal homeostasis. We hypothesize here that fecal miRNAs are a third player in the microbiota-host interaction that can mediate direct microbiota alterations that will in turn impact the host.