The purpose of this work is to investigate the link between an altered intestinal mcro-biota or dysbiosis and chronic inflammatory disorders, in particular inflammatory bowel disease (IBD). Along with probiotics, faecal microbiota transplantation (FMT) opts to be a promising therapeutic treatment for restoring the bacterial homeostasis of the hu-man intestine and reducing the risk of colorectal carcinogenesis. Microbiota is the com-plex microbial flora that resides in the gut establishing a mutually beneficial relation-ship. Alteration of the microbiota’s composition, termed as dysbiosis, may lead to pathological conditions. Treatment with probiotics can restore the normal commensal flora in IBD. Intestinal microbiota affects the circadian rhythm which in turn regulates the expression of different genes in GALT (gut associated lymphoid tissue) playing a role in the prevention of inflammation and colorectal cancer (CRC) progression. This article highlights the involvement of different microbial strains in the pathogenesis of dysbiosis and in the creation of a carcinogenic milieu caused by an altered stimulation of the immune system. Therapies targeting the equilibrium of the microbiota to switch off chronic inflammation and prevent the progression to CRC seem to be a promising therapeutic tool for a variety of inflammation-associated diseases.