The gut microbiota plays a crucial role in human health, influencing various physiological processes and immune system modulation. Dysbiosis, or an imbalance in the gut microbiome, disrupts essential functions and contributes to diseases such as inflammatory bowel diseases (IBDs) like ulcerative colitis and Crohn's disease, as well as obesity and other systemic conditions. This review highlights key findings related to the gut microbiota in modern multifactorial inflammatory conditions and the challenges posed by antibiotic-driven dysbiosis, particularly in *Clostridioides difficile* infections. It emphasizes the development of novel therapies like fecal microbiota transplantation (FMT) and biotherapeutic drugs to combat these infections. The restoration of a healthy gut microbiome through dietary interventions, probiotics, prebiotics, and novel approaches is also discussed. The review covers the etiology and pathogenesis of Crohn's disease, the clinical significance and diagnostic procedures, and treatment options, including probiotics and FMT. It also explores ulcerative colitis, the role of specific bacterial species, and the impact of diet and metabolic changes. The special case of *Clostridioides difficile* infections is discussed, along with the safety concerns and alternative therapies for FMT. Finally, the review examines the benefits of probiotics, prebiotics, and fermented foods in restoring gut health and managing gut-related diseases.The gut microbiota plays a crucial role in human health, influencing various physiological processes and immune system modulation. Dysbiosis, or an imbalance in the gut microbiome, disrupts essential functions and contributes to diseases such as inflammatory bowel diseases (IBDs) like ulcerative colitis and Crohn's disease, as well as obesity and other systemic conditions. This review highlights key findings related to the gut microbiota in modern multifactorial inflammatory conditions and the challenges posed by antibiotic-driven dysbiosis, particularly in *Clostridioides difficile* infections. It emphasizes the development of novel therapies like fecal microbiota transplantation (FMT) and biotherapeutic drugs to combat these infections. The restoration of a healthy gut microbiome through dietary interventions, probiotics, prebiotics, and novel approaches is also discussed. The review covers the etiology and pathogenesis of Crohn's disease, the clinical significance and diagnostic procedures, and treatment options, including probiotics and FMT. It also explores ulcerative colitis, the role of specific bacterial species, and the impact of diet and metabolic changes. The special case of *Clostridioides difficile* infections is discussed, along with the safety concerns and alternative therapies for FMT. Finally, the review examines the benefits of probiotics, prebiotics, and fermented foods in restoring gut health and managing gut-related diseases.