The article reviews the growing evidence that dysbiosis of the gut microbiota is associated with both intestinal and extra-intestinal disorders. Intestinal disorders include inflammatory bowel disease, irritable bowel syndrome (IBS), and coeliac disease, while extra-intestinal disorders include allergy, asthma, metabolic syndrome, cardiovascular disease, and obesity. The establishment of a healthy relationship between the colonic microbiota, their metabolic products, and the host immune system is crucial for maintaining intestinal homeostasis. Recent studies have identified specific bacterial species associated with a healthy microbiota, particularly those residing in the mucus layer of the colon. These bacteria influence host cellular homeostasis and may trigger inflammatory mechanisms. Additionally, perturbations in the gut microbiota are linked to the development of colorectal cancer, possibly through the production of carcinogenic metabolites from high-protein diets. The article also discusses the impact of diet on the gut microbiome, highlighting the production of small molecules that mimic or act as neurosignallers or neurotransmitters. Probiotic interventions have shown potential in altering psychological endpoints in both humans and rodent models, suggesting that CNS-related co-morbidities associated with GI disease may originate in the intestine due to microbial dysbiosis. The review outlines the current evidence on how the gut microbiota contributes to disease development and explores potential strategies for modulating the composition of the colonic microbiota to ameliorate disease activity through bacterial intervention. Keywords include microbiome, short-chain fatty acids, gut health, colonic metabolome, gut-brain-axis, and inflammation.The article reviews the growing evidence that dysbiosis of the gut microbiota is associated with both intestinal and extra-intestinal disorders. Intestinal disorders include inflammatory bowel disease, irritable bowel syndrome (IBS), and coeliac disease, while extra-intestinal disorders include allergy, asthma, metabolic syndrome, cardiovascular disease, and obesity. The establishment of a healthy relationship between the colonic microbiota, their metabolic products, and the host immune system is crucial for maintaining intestinal homeostasis. Recent studies have identified specific bacterial species associated with a healthy microbiota, particularly those residing in the mucus layer of the colon. These bacteria influence host cellular homeostasis and may trigger inflammatory mechanisms. Additionally, perturbations in the gut microbiota are linked to the development of colorectal cancer, possibly through the production of carcinogenic metabolites from high-protein diets. The article also discusses the impact of diet on the gut microbiome, highlighting the production of small molecules that mimic or act as neurosignallers or neurotransmitters. Probiotic interventions have shown potential in altering psychological endpoints in both humans and rodent models, suggesting that CNS-related co-morbidities associated with GI disease may originate in the intestine due to microbial dysbiosis. The review outlines the current evidence on how the gut microbiota contributes to disease development and explores potential strategies for modulating the composition of the colonic microbiota to ameliorate disease activity through bacterial intervention. Keywords include microbiome, short-chain fatty acids, gut health, colonic metabolome, gut-brain-axis, and inflammation.