**Abstract**

There are mounting evidences showing the relation of chronic inflammatory and autoimmune diseases with the uncontrolled intensification of gut dysbiosis. This position asserts that an elevated presence of pathogens and bacterial, fungal, and viral components is directly involved in inflammatory metabolic diseases with a strong alteration of autoimmune components such as in inflammatory bowel syndrome (IBS), ulcerative colitis, and Crohn's disease. Furthermore, the increase of unbalanced enteric microbiota is also connected to other types of conditions of metabolic origin such as diabetes mellitus, atherosclerosis, and osteo-degenerative conditions. As a matter of fact, evidence confirmed that gut damages histologically inspected revealed a situation with high expression of pro-inflammatory cytotumor necrosis factor-alpha (TNF-α), and IL1β, IL-2, IL-4, IL-6, and IL-17 together with high level of mucin-2. This chapter focuses on diverse topics related to microbiota dysfunction and systemic health condition and regenerative capacity and the therapeutic role of probiotics in gut health and disease emphasizing the potential beneficial role of probiotics in idiopathic inflammatory metabolic diseases. In brief, outcomes demonstrate that an intimate relationship between microbiota, metabolism, tissue/cellular damages, and regeneration is standing. Within this scenario, the gut certainly plays a big part of the regenerative mechanisms in translational medicine.

**Keywords:** inflammatory bowel syndrome, ulcerative colitis, Crohn's disease, gut dysbiosis, short-chain fatty acids, central nervous system, experimental autoimmune encephalopathy, vagus nerve, tumor necrosis factor-alpha, IL1β, IL-2, IL-4, IL-6, IL-17, mucin-2, probiotics
