Table 3. Negative binomial model results for IBD phenotype, genotype and clinical covariates at the phylum/subphylum level.
Variables with significant effects are bolded.
| Actinobacteria | Log fold change | p -value | FDR |
|---|---|---|---|
| Main effects1 | |||
| ileal CD | 2.055 | <0.0001 | <0.0001 |
| Colitis | 1.368 | <0.0001 | <0.0001 |
| Duration IBD | -0.064 | <0.0001 | <0.0001 |
| Batch | -1.194 | <0.0001 | <0.0001 |
| + C. difficile fecal toxin | -2.878 | 0.0056 | 0.0083 |
| Anti TNF alpha | -0.889 | 0.0015 | 0.0026 |
| Current smoker | -0.333 | 0.1081 | 0.1179 |
| Age | 0.001 | 0.9801 | 0.9801 |
| First order interactions | |||
| + C. difficile fecal toxin*Current smoker | 2.806 | 0.0009 | 0.0017 |
| + C. difficile fecal toxin *Age | 0.530 | 0.0124 | 0.0149 |
| Duration IBD * Anti TNF alpha | 0.008 | 0.0064 | 0.0083 |
| Firmicutes/Clostridia/Lachnospiraceae | Log fold change | p -value | FDR |
| Main effects | |||
| Immunomodulators | -0.347 | 0.0068 | 0.0068 |
| Firmicutes/Clostridia/Ruminococcaceae | Log fold change | p -value | FDR |
| Main effects | |||
| ileal CD | -0.989 | 0.0001 | 0.0002 |
| Colitis | -0.244 | 0.2714 | 0.2714 |
| Age | -0.017 | 0.0030 | 0.0032 |
| Immunomodulators | 1.879 | 0.0160 | 0.0224 |
| BMI | 0.0282 | 0.0674 | 0.0787 |
| First order interactions | |||
| Immunomodulators * BMI | -0.939 | 0.0012 | 0.0027 |
| Firmicutes/Clostridia/Other | Log fold change | p -value | FDR |
| NOD2R | 0.569 | 0.0028 | 0.0042 |
| ORMDL3R | 0.716 | 0.0001 | 0.0003 |
| XBP1R | -1.000 | 0.0001 | 0.0003 |
| + C. difficile fecal toxin | 1.365 | 0.0001 | 0.0003 |
| Steroids | 0.606 | 0.0026 | 0.0042 |
| Immunomodulators | -2.387 | 0.0027 | 0.0042 |
| BMI | -0.0416 | 0.0065 | 0.0081 |
| Colon Cancer | -0.0384 | 0.8703 | 0.8703 |
| Current smoking | -0.3546 | 0.2724 | 0.3143 |
| First order interactions | |||
| Current smoking * 5-ASA | 1.9875 | <0.0001 | 0.0002 |
| Current smoking * Steroids | -1.287 | 0.006 | 0.0081 |
| Immunomodulators * BMI | 0.1074 | 0.0002 | 0.0005 |
| Firmicutes/Bacilli | Log fold change | p-value | FDR |
| Main effects | |||
| ileal CD | 1.7384 | <0.0001 | <0.0001 |
| Colitis | 1.2696 | <0.0001 | <0.0001 |
| Batch | -0.9925 | <0.0001 | <0.0001 |
| 5-ASA | -0.8868 | 0.0049 | 0.0057 |
| Steroids | -0.3359 | 0.2659 | 0.2659 |
| First order interactions | |||
| 5-ASA*Steroids | 1.4087 | 0.0014 | 0.0019 |
| Proteobacteria | Log fold change | p-value | FDR |
| Main effects | |||
| ileal CD | 0.6767 | <0.0001 | 0.0001 |
| Colitis | 0.5257 | 0.002 | 0.0023 |
| NOD2R | -1.0788 | 0.0002 | 0.0003 |
| ORMDL3R | -0.2539 | 0.1433 | 0.1433 |
| First order interactions | |||
| NOD2R* ORMDL3R | 1.3856 | <0.0001 | 0.0001 |