Crohn’s disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease’s severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity. Methods: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed. Results: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species. Conclusions: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.

Background/Objectives: Inflammatory bowel diseases (IBDs) are an increasingly important global health problem, yet Central Asia remains underrepresented in international IBD data. To evaluate the clinical and demographic characteristics of patients included in the national multicenter clinical IBD registry of the Republic of Kazakhstan (IBD Registry) according to disease activity at registry enrollment visit and to identify factors associated with active IBD at that time. Methods: We conducted a cross-sectional analysis of the registry enrollment visit data from the national multicenter clinical IBD registry of the Republic of Kazakhstan. The study included patients with ulcerative colitis (UC) and Crohn’s disease (CD) registered between 2021 and 2024. Disease activity at the registry enrollment visit was assessed using the full Mayo score for UC and the Harvey–Bradshaw index for CD. Univariable and multivariable logistic regression analyses were performed to identify factors associated with active disease. Results: The analysis included 1521 patients with IBD, 68.4% with ulcerative colitis and 31.6% with Crohn’s disease. At the registry enrollment visit, 77.5% of patients had clinically active disease. In UC, active disease was independently associated with rural residence (aOR 2.11; 95% CI 1.25–3.56), ≥2 exacerbations per year (aOR 3.47; 95% CI 2.18–5.51), current corticosteroid therapy (aOR 5.96; 95% CI 3.04–11.69), and immunosuppressive therapy (aOR 2.71; 95% CI 1.15–6.38), whereas rare exacerbations were associated with lower odds of activity (aOR 0.41; 95% CI 0.23–0.73). In CD, active disease was independently associated with ≥2 exacerbations per year (aOR 2.41; 95% CI 1.47–3.95), colonic (L2) location (aOR 2.32; 95% CI 1.25–4.30), ileocolonic (L3) location (aOR 2.24; 95% CI 1.25–4.04), extraintestinal manifestations (aOR 2.88; 95% CI 1.68–4.93), and current corticosteroid therapy (aOR 1.77; 95% CI 1.03–3.05), whereas immunosuppressive therapy was associated with lower odds of active disease (aOR 0.46; 95% CI 0.24–0.89). Biologic therapy was not independently associated with disease activity in either UC or CD. Conclusions: A high proportion of patients treated at participating secondary and tertiary centers had clinically active IBD at registry enrollment. The profiles of factors associated with activity differed between UC and CD, while frequent exacerbations were consistently associated with active disease in both conditions. These findings should be interpreted as cross-sectional associations rather than causal or prognostic relationships, particularly for treatment-related factors.