Table 2.
The effects of inflammation, antibiotics, outcome, and sample location on the transcriptome and microbiome
| Transcriptome | Microbiome | |||
|---|---|---|---|---|
| PPI | Pouch | PPI | Pouch | |
| Inflammation score | 19% | 22% | 0% | 5% |
| Antibiotics | 0% | 0% | 41% | 2% |
| Outcome | 0% | 15% | 3% | 3% |
| Location | 45% | 1% | ||
This table shows the percentages of the transcriptome and microbiome that are differentially expressed (FDR <0.05) with respect to inflammation score (continuous scale 0–12), antibiotics usage (yes/no), outcome (AP, NP, CP, CDL), and sampling location (pouch or pre-pouch ileum). The microbiome is extensively shifted by antibiotics usage with minor shifts by outcome and location, whereas the host transcriptome is extensively shifted between locations and by inflammation. See also (Additional file 4, Additional file 3D to I).