Table 3.
Linear Mixed-Effects Modeling of Time-Dependent Alterations in the FARMM Study Comparing Alterations in the Relative Abundance of Genes in the cai Operon Across the 3 Diets Before and After Antibiotic Treatment
| KEGG Orthology Identifier | Gene name | Term | Value | SE | Degrees of Freedom | t value | P value | FDR | |
|---|---|---|---|---|---|---|---|---|---|
| Antibiotic treatment | K05245 | caiT | Study day | -0.70 | 0.26 | 41 | -2.72 | .01 | 0.022 |
| K08299 | caiD | Study day | -1.13 | 0.25 | 41 | -4.43 | .00 | 0.00018 | |
| Postantibiotics | K02182 | caiC | Study day | 0.43 | 0.08 | 157 | 5.32 | .00 | 1.1e-06 |
| K05245 | caiT | Study day | 0.56 | 0.08 | 157 | 7.19 | .00 | 1.9e-10 | |
| K05245 | caiT | Study day | -0.36 | 0.11 | 157 | -3.19 | .00 | 0.036 | |
| K08277 | caiF | Study day | 0.60 | 0.08 | 157 | 7.18 | .00 | 1.9e-10 | |
| K08279 | caiE | Study day | 0.54 | 0.08 | 157 | 6.96 | .00 | 4.6e-10 | |
| K08297 | caiA | Study day | 0.50 | 0.08 | 157 | 6.12 | .00 | 2.6e-08 | |
| K08298 | caiB | Study day | 0.58 | 0.08 | 157 | 7.18 | .00 | 1.9e-10 | |
| K08299 | caiD | Study day | 0.51 | 0.08 | 157 | 6.63 | .00 | 2.1e-09 |
FDR, false discovery rate. See Figure 3C.