Part 1 of this review discussed the connection between the human gut microbiota and health. Manipulation of the intestinal microbiota holds promise as a prospective therapy for gut dysbiosis, ameliorating symptoms of gastrointestinal and systemic diseases and restoring health. The concept of probiotics has existed for more than 100 y, and modern research methods have established sound scientific support for the perceived benefits of probiotic bacteria, which mainly include Lactobacillus and Bifidobacterium genera. On the basis of these evidence-based functional approaches, dietary interventions that supplement the normal diet with probiotics or prebiotics are now considered as potentially viable alternatives or adjuncts to the use of steroids, immunosuppressants, and/or surgical interventions. Studies investigating the impact on gastrointestinal disorders, such as diarrhea, inflammatory bowel disease (IBD), irritable bowel syndrome (IBS); and systemic metabolic diseases, such as type 2 diabetes and obesity, in response to the use of probiotics and prebiotics are reviewed. Further, fecal microbial transplantation (FMT) is discussed as an exciting development in the treatment of gut dysbiosis using microbes.