Abstract

The intestinal microbiome plays a central role in the pathogenesis of inflammatory bowel disease (IBD), which 
includes Crohn’s disease and ulcerative colitis. Dysbiosis, characterized by reduced microbial diversity, expansion 
of pro-inflammatory taxa, and depletion of protective commensals such as Faecalibacterium prausnitzii, is a 
hallmark of IBD and contributes to chronic intestinal inflammation. Altered microbiota composition influences 
immune regulation, barrier function, and metabolic activity, perpetuating the cycle of inflammation and mucosal 
injury. Environmental factors, including diet, antibiotics, and lifestyle, further modulate microbial ecosystems, 
shaping disease onset and progression. Therapeutic strategies to restore microbial balance, such as dietary 
interventions, probiotics, prebiotics, and fecal microbiota transplantation (FMT), show promise as adjuncts to 
conventional pharmacological treatments. Advances in metagenomics, metabolomics, and multi-omics integration 
are driving personalized approaches to IBD care, yet challenges remain in standardization, reproducibility, and 
ethical considerations. This review summarizes current evidence on microbiome alterations in IBD, underlying 
mechanisms, therapeutic strategies, and the potential for microbiome-targeted precision medicine. 
Keywords: Inflammatory bowel disease, Gut microbiome, Dysbiosis, Probiotics and FMT, and Precision 
medicine.