Comparative Metagenomics of the Gut Microbiome in IBD vs IBS Patients

Background: Inflammatory bowel disease and irritable bowel syndrome commonly present with overlapping gastrointestinal symptoms but differ substantially in their underlying mechanisms. Objective: To compare the gut microbiome composition and functional metagenomic profiles of patients with inflammatory bowel disease and irritable bowel syndrome. Methodology: This comparative cross-sectional study was conducted at Allama Iqbal Teaching Hospital, Dera Ghazi Khan from June 2024 to June 2025 and included 170 patients equally divided into inflammatory bowel disease (n=85) and irritable bowel syndrome (n=85) groups. Results: The inflammatory bowel disease group had significantly higher mean C-reactive protein (18.6 ± 9.5 vs. 4.2 ± 2.1 mg/L), erythrocyte sedimentation rate (32.4 ± 13.7 vs. 13.8 ± 6.5 mm/hour), and fecal calprotectin levels (416.8 ± 154.6 vs. 64.3 ± 32.8 µg/g) than the irritable bowel syndrome group; all p<0.001. Microbial diversity was significantly lower in inflammatory bowel disease, with reduced Shannon (3.28 ± 0.64 vs. 4.12 ± 0.58) and Simpson indices (0.73 ± 0.09 vs. 0.84 ± 0.07); both p<0.001. Patients with inflammatory bowel disease had lower Firmicutes abundance (36.8 ± 10.4% vs. 49.7 ± 11.3%) and higher Proteobacteria abundance (21.4 ± 7.8% vs. 9.3 ± 4.5%); both p<0.001. Conclusion: It is concluded that inflammatory bowel disease is associated with markedly reduced microbial diversity, depletion of beneficial bacteria, enrichment of pro-inflammatory taxa, and altered microbial metabolic pathways compared with irritable bowel syndrome.