Abstract
Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a chronic gastrointestinal disorder characterized by immune dysregulation and microbial imbalance. This study presents a gut microbiome analysis of Kazakhstani IBD patients, comparing stool microbiota from 132 IBD patients and their 132 non-IBD relatives using 16S rRNA sequencing. The results revealed a significant reduction in microbial diversity and distinct dysbiosis patterns in UC and CD. UC was associated with an overrepresentation of pathogenic genera (e.g., Streptococcus, Haemophilus ), while CD exhibited increased abundance of metabolically adaptive taxa (e.g., Olsenella, Flavonifractor ). Functional profiling revealed an increase in predicted pathways related to oxidative stress response and antibiotic biosynthesis, together with a reduction in steroid biosynthesis and bacterial motility pathways in UC. Random forest models using microbial and functional features achieved good classification performance (AUC = 0.83 and AUC = 0.75, respectively), identifying candidate diagnostic biomarkers. Correlation analyses linked microbial shifts with systemic inflammation (CRP, ESR), disease duration, and depressive symptoms, suggesting possible involvement of the gut–immune–brain axis. These findings underscore the microbiome’s diagnostic and therapeutic potential in IBD and highlight the need for personalized, microbiota-directed strategies tailored to regional microbial profiles.