P143 Evaluating intestinal biopsy preservation and storage methods to facilitate large-scale microbiome research in inflammatory bowel disease (IBD)
Bibliographic record
Abstract
<h3>Introduction</h3> Large multicentre studies are key to understanding complex relationships between the gut microbiome and outcomes in IBD. Interrogating the mucosal microbiome may identify biological signals not captured by stool, which mostly reflects distal colon. Gold standard tissue cryopreservation by ‘flash freezing’ is likely to limit large study feasibility. We aimed to compare gold standard and pragmatic mucosal biopsy storage vs stool. <h3>Methods</h3> We collected endoscopic recto-sigmoid biopsies and paired stool (prior to bowel cleansing) from 20 adults with IBD (ethical approval: Wales REC5, ref 21/WA/0228). Biopsy preservation and storage conditions are shown in <i>figure 1</i>. Microbiota was sequenced on the MiSeq (Illumina) platform using the 16S rRNA gene (V4 region). Statistical analyses were performed in R, including decontam package for FFPE analyses. <h3>Results</h3> Gut microbiome was consistent between proximal and distal biopsies suggesting any within-patient variation observed would be reflective of storage condition, not location. There was no significant difference in alpha diversity (richness, P=0.99; Shannon index, P=0.99) or microbiota profile (P=1.00; R2=0.01) of reagent-preserved vs gold standard tissue. Whilst FFPE community structure was not significantly different to stool, there was significant dissimilarity vs other tissue (P=0.001, R2 0.23). This was driven by differential relative abundance of obligate gut anaerobes; <i>Faecalibacterium</i>, <i>Anaerostipes</i> and Lachnospiraceae. Despite this, tissue microbiota grouped by participant (P=0.001, R2=0.56) regardless of preservation and storage condition. FFPE richness (P=0.11) and Shannon index (P=0.09) was comparable to other tissue conditions. <h3>Conclusions</h3> Preservative reagents are a convenient alternative to flash freezing tissue in large microbiome studies. Whilst less comparable, FFPE specimens provide potential for microbiome studies using historically banked samples. Access to tissue for microbiome and other omic analysis will evolve mechanistic understanding of IBD.
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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 | 0.025 | 0.031 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.015 | 0.004 |
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".