Microbial Patterns in Newly Diagnosed Inflammatory Bowel Disease Revealed by Presence and Transcriptional Activity - Relationship to Diagnosis and Outcome

Vatn, SS; Hansen, SH; Tannæs, TM; Brackmann, S; Olbjørn, C; Bergemalm, D; Keita, ÅV; Gomollon, F; Detlie, TE; Kalla, R; Satsangi, J; Jahnsen, J; Vatn, MH; Halfvarson, J; Hov, JR; Ricanek, P; Moen, AEF

Journal article

Microbial Patterns in Newly Diagnosed Inflammatory Bowel Disease Revealed by Presence and Transcriptional Activity - Relationship to Diagnosis and Outcome

Abstract:: BackgroundAs part of the IBD Character initiative, we examined an inception cohort and investigated mucosal microbiota composition and transcriptional activity in relation to clinical outcomes.MethodsA cohort of 237 individuals were included from five countries: Crohn's disease (CD, n = 72), ulcerative colitis (UC, n = 57), symptomatic non-IBD controls (SC, n = 78) and healthy controls (HC, n = 30). Rectal/colonic biopsies were obtained at inclusion, and DNA and RNA were extracted from the same biopsy and examined by sequencing the 16S rRNA V4 region.ResultsBeta diversity measurements separated IBD from both HC and SC. IBD and SC exhibited reduced intra-individual diversity compared with HC. When comparing taxonomy at DNA and RNA level, six bacteria were found to differ in abundance and/or transcriptional activity between IBD and symptomatic control, while there were 14 and three between symptomatic control and CD and UC, respectively. A limited number of bacterial taxa were responsible for the largest difference between presence and activity, separating patients and controls. Multiple bacterial taxa were associated with treatment escalation in both UC and CD. Machine-learning models separated IBD from symptomatic controls and treatment escalators from non-escalators (AUC >0.8). However, the differential effects were mainly driven by clinical biomarkers, such as f-calprotectin, s-albumin, and b-hemoglobin.ConclusionDifferences between presence and transcriptional activity were found among multiple taxa when assessing 16S rRNA at DNA and RNA level. Symptomatic controls were more similar to the IBD patients compared to HC. The analyses suggest that the mucosal microbiota carries a moderate diagnostic and predictive potential, outcompeted by f-calprotectin.

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

Vatn, S. S., Hansen, S. H., Tannæs, T. M., Brackmann, S., Olbjørn, C., Bergemalm, D., Keita, Å. V., Gomollon, F., Detlie, T. E., Kalla, R., Satsangi, J., Jahnsen, J., Vatn, M. H., Halfvarson, J., Hov, J. R., Ricanek, P., & Moen, A. E. F. (2025). Microbial Patterns in Newly Diagnosed Inflammatory Bowel Disease Revealed by Presence and Transcriptional Activity - Relationship to Diagnosis and Outcome. Clinical and Experimental Gastroenterology, 18, 103–119.

MLA Style

Vatn, S. S., et al. “Microbial Patterns in Newly Diagnosed Inflammatory Bowel Disease Revealed by Presence and Transcriptional Activity - Relationship to Diagnosis and Outcome.” Clinical and Experimental Gastroenterology, vol. 18, Taylor and Francis Group, 2025, pp. 103–19.

Chicago Style

Vatn, SS, SH Hansen, TM Tannæs, S Brackmann, C Olbjørn, D Bergemalm, ÅV Keita, et al. 2025. “Microbial Patterns in Newly Diagnosed Inflammatory Bowel Disease Revealed by Presence and Transcriptional Activity - Relationship to Diagnosis and Outcome.” Clinical and Experimental Gastroenterology 18: 103–19.
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