P789 Microbiome composition is altered in patients with IBD independent of endoscopic activity
Bibliographic record
Abstract
Background: Genetic and microbial heterogeneity in inflammatory bowel disease (IBD) are likely important in pathogenesis and in determining phenotype classification into: Crohn's disease (CD), ulcerative colitis (UC) and IBD unclassified (IBDU). This study aims to characterise intestinal mucosal microbial profiles and potential association with IBD phenotypic characteristics. Methods: IBD patients and healthy controls (HC) were recruited from a tertiary care IBD center on the day of colonoscopy performed for disease activity assessment. Clinical and demographic data were recorded. Quiescent IBD was defined as partial Mayo 0 or SES-CD 0–2. Amplicon sequencing of the V4 region of 16s rRNA bacterial DNA was completed on Illumina MiSeq platform and sequences processed using the QIIME pipeline. Alpha diversity was calculated using Chao1 index after rarefaction at 8,500 reads per sample and associations addressed using parametric t-test. Principle coordinate analysis was conducted using Bray-Curtis as the beta diversity metric and significance tested using Adonis test. Taxa analysis was completed with Kruskal Wallis test. Results: 263 sigmoid colon biopsies (UC n=101, CD n=96, HC n=48) were analysed. HC showed separation of beta diversity (p<0.001, R<0.15) and greater alpha diversity (0.001<p<0.04) than quiescent CD (n=31), and quiescent UC (n=37) respectively. In HC, taxa analysis identified increased Firmicutes (q=0.001), and reduced Fusobacteria relative abundance (RA) (q=0.04) and at genus level, reduced Actinobacteria microbacteria RA (q<0.04) relative to quiescent UC and CD. We also compared microbiome profiles between IBD phenotypes. In quiescent disease, patients with CD involving the colon clustered with UC patients on a PCoA plot with no significant differences in taxa, however alpha diversity was reduced in CD relative to UC. Patients with endoscopic activity and remission were subsequently combined. CD patients had persistent reduced alpha diversity (p=0.0004), and also weak separation from UC patients by beta diversity metrics (q<0.02, R=0.01). Taxa analysis identified a trend of increased Fusobacteria and Proteobacteria RA (q=0.059), and reduced Coribactericeae adlercreutzia RA in colonic CD compared with UC (q=0.03). Conclusions: IBD patients have altered microbiome profiles relative to HC in active and quiescent disease, although histological activity was not captured here. Both UC and CD phenotypes had reduced Firmicutes and increased Actinobacteria abundance relative to HC, indicating microbiome dysbiosis in the absence of endoscopic activity. We show reduced alpha diversity in CD phenotypes relative to UC despite no difference in taxa of quiescent patients.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".