P1319 Multi-omic modelling of antibiotic perturbed faecal microbial communities demonstrates reduced microbial resilience in IBD
Bibliographic record
Abstract
Abstract Background Excessive antibiotic use is a risk factor in IBD, due to the impact on the gastrointestinal microbiota, but the extent of impact on microbial metabolite production is unknown. Here we investigate the impact of ciprofloxacin (CIP) and metronidazole (MTZ) on gut microbiota structure/function in a healthy donor and a new-onset therapeutic naïve IBD patient. We also investigate the use of autologous faecal microbiota transplant (aFMT) as a microbial therapeutic to assist recovery of the gut ecosystem. Methods Donor faecal specimens (IBD or healthy) were used to inoculate twin chemostat vessels. Following community stabilisation, vessels were dosed daily with CIP or MTZ for 7 days. In the healthy donor vessel, 4 doses of aFMT were administered over 7 days (post antibiotics) followed by a 7-day recovery. In the IBD vessels no FMT was administered. Vessels were sampled daily to monitor microbial profiles (16S rRNA sequencing) and short chain fatty acid (SCFA) profiles (GC-MS). Results CIP in the healthy vessel caused a significant depletion of acetate, butyrate and propionate, remaining significantly depleted during aFMT. CIP dosing also resulted in an enrichment of Escherichia-Shigella and Enterobacter and a loss of Akkermansia, Faecalibacterium and Bacteroides. During recovery acetate and propionate recovered whilst butyrate remained depleted (p=0.004). In the healthy MTZ vessel, acetate increased during antibiotic dosing and was restored following aFMT. Butyrate decreased during MTZ dosing and remained significantly decreased (p<0.031). Propionate levels also reduced following MTZ but were found in highest abundance during aFMT and recovery phases (p<0.038). Parabacteroides increased during MTZ dosing which subsequently decreased to stable abundance. Akkermansia was significantly increased in recovery phase compared to aFMT and stability phases. In the IBD donor, CIP caused a significant reduction in 10 SCFAs and several taxa including Bacteroides and Dialister genera alongside an enrichment of Enterococcus, Lachnospiraceae, Anaerofilum and Eisenbergiella. MTZ treatment resulted in a less dramatic reduction in SCFAs. Microbial community changes included an enrichment of Escherichia-Shigella, Enterococcus and Parasutterella and a depletion of Alistipes and Dialister. Conclusion CIP and MTZ significantly depleted levels of beneficial genera and reduced the abundance of SCFAs. Neither donor community was able to fully restore composition or function. aFMT modulated the healthy donor microbial communities to a "new healthy". Further investigation into long-term antibiotic treatment and the use of microbial therapeutics is needed to fully understand this relationship in the context 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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
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".