Table 3. Taxa to the genus level with ≥2-fold change in relative abundance from baseline to end of treatment (EOT) with vancomycin or ridinilazole.
| Vancomycin | Ridinilazole | |||||||
|---|---|---|---|---|---|---|---|---|
| Taxa | Baseline | EOT | Fold change | q value | Baseline | EOT | Fold change | q value |
| Actinobacteria | 1.49E-04 | 9.57E-05 | 4.9 | 0.021 | ||||
| c_Actinobacteria g_Bifidobacterium | 2.14E-04 | <LLD | 4.5 | 0.029 | ||||
| c_Coriobacteria f_Coriobacteriaceae | 1.35E-04 | <LLD | 2.8 | 0.025 | ||||
| Bacteroidetes | 7.96E-01 | 4.49E-04 | 1773.5 | 0.006 | ||||
| f_Bacteroidaceae g_Bacteroides | 7.36E-01 | 1.17E-04 | 6274.8 | 0.008 | ||||
| f_Porphyromonadaceae | 5.42E-03 | <LLD | 113.5 | 0.034 | ||||
| Firmicutes | ||||||||
| c_Bacilli f_Lactobacillaceae | 4.79E-05 | 2.43E-03 | 50.8 | 0.019 | ||||
| c_Clostridia f_Clostridiaceae g_Clostridium | 2.39E-04 | <LLD | 5.0 | 0.027 | 9.57E-04 | 9.57E-05 | 10.0 | 0.002 |
| c_Clostridia f_Lachnospiraceae | 6.76E-02 | <LLD | 1415.8 | 0.003 | ||||
| g_Blautia | 7.59E-03 | <LLD | 158.9 | 0.004 | ||||
| g_Coprococcus | 6.55E-04 | <LLD | 13.7 | 0.007 | ||||
| g_Dorea | 4.98E-04 | <LLD | 10.4 | 0.016 | ||||
| g_Roseburia | 1.91E-04 | <LLD | 4.0 | 0.022 | ||||
| g_Ruminococcus | 3.23E-03 | <LLD | 67.6 | 0.014 | ||||
| c_Clostridia f_Peptostreptococcaceae | 8.55E-04 | <LLD | 17.9 | 0.005 | 1.53E-03 | <LLD | 35.8 | <0.001 |
| Clostridium difficile | 1.91E-04 | <LLD | 4.0 | 0.026 | 7.18E-04 | <LLD | 15.0 | 0.001 |
| c_Clostridia f_Ruminococcaceae | 2.72E-02 | <LLD | 570.2 | 0.002 | 4.13E-02 | 2.82E-03 | 14.6 | 0.002 |
| g_Faecalibacterium | 1.46E-03 | <LLD | 30.5 | 0.013 | ||||
| g_Oscillospira | 2.14E-03 | <LLD | 44.8 | 0.015 | ||||
| g_Ruminococcus | 1.91E-04 | <LLD | 4.0 | 0.021 | ||||
| c_Clostridia f_Veillonellaceae g_Veillonella | 2.51E-03 | 3.05E-02 | 12.2 | 0.025 | ||||
| c_Erysipelotrichi f_Erysipelotrichiaceae | 2.22E-03 | <LLD | 46.6 | 0.005 | ||||
| g_Eubacterium | 8.13E-04 | <LLD | 17.0 | 0.022 | ||||
| Proteobacteria | 2.86E-02 | 6.55E-01 | 22.9 | 0.002 | ||||
| f_Enterobacteriaceae | 2.16E-03 | 4.73E-01 | 219.4 | 0.001 | ||||
| g_Citrobacter | 4.79E-05 | 1.23E-02 | 257.6 | 0.012 | ||||
| g_Enterobacter | <LLD | 7.60E-04 | 15.9 | 0.008 | ||||
| g_Erwinia | <LLD | 4.06E-04 | 8.5 | 0.010 | ||||
| g_Escherichia | 2.34E-04 | 1.30E-02 | 55.6 | 0.009 | ||||
| g_Klebsiella | 4.79E-05 | 0.05445 | 1137.6 | 0.010 | ||||
| g_Salmonella | <LLD | 3.58E-04 | 7.5 | 0.011 | ||||
| g_Serratia | <LLD | 5.74E-04 | 12.0 | 0.016 | ||||
| g_Trabulsiella | <LLD | 1.35E-04 | 2.8 | 0.027 | ||||
| f_Pasteurellaceae g_Haemophilus | 2.14E-04 | <LLD | 4.5 | 0.033 | ||||
| Decrease | Increase | |||||||
| <5 fold | <5 fold | |||||||
| >5 to <10 fold | >5 to <10 fold | |||||||
| >10 fold | >10 fold | |||||||
| >100 fold | >100 fold | |||||||
| >1000 fold | >1000 fold | |||||||
P-values were determined by the Wilcoxon rank sum test, following which q values were derived using the Benjamini-Hochberg procedure to hold the false discovery rate to 0.10
c = class, o = order, f = family, g = genus, LLD = lower limit of detection