Table 3.
Several species among the Lachnospiraceae family and others had significant changes in normalized abundance with antibiotic treatment in the neutropenic subjects but not in the controls based on DESeq2 analysis.
| Family | Genus | Species | log2FoldChange | p value | p adj |
|---|---|---|---|---|---|
| Differentially abundant at baseline/recovery versus on antibiotics in neutropenic but not control subjects. (positive log2FoldChange means more abundant at baseline/recovery) | |||||
| Clostridiaceae | Clostridium sensu stricto 1 | NA | 24.5728 | 9.57E−17 | 1.93E−15 |
| Lachnospiraceae | Roseburia | intestinalis | 24.2399 | 2.46E−16 | 3.95E−15 |
| Lachnospiraceae | Roseburia | inulinivorans | 24.2319 | 2.52E−16 | 3.95E−15 |
| Veillonellaceae | Dialister | invisus | 23.0949 | 5.81E−15 | 5.85E−14 |
| Ruminococcaceae | Incertae Sedis | NA | 22.1833 | 6.54E−14 | 5.42E−13 |
| Lachnospiraceae | Coprococcus | comes | 22.0889 | 8.12E−14 | 6.36E−13 |
| Lachnospiraceae | Lachnospiraceae NK4A136 group | NA | 8.3500 | 0.0034 | 0.0221 |
| Peptostreptococcaceae | Romboutsia | NA | 7.4296 | 0.0073 | 0.0445 |
| Lachnospiraceae | Anaerostipes | hadrus | 26.6619 | 3.97E−21 | 5.59E−19 |
| Ruminococcaceae | Ruminococcus | bromii | 25.9072 | 1.92E−18 | 6.76E−17 |
| Lachnospiraceae | [Eubacterium] fissicatena group | NA | 25.5143 | 6.19E−18 | 1.75E−16 |
| Lachnospiraceae | Agathobacter | NA | 23.2200 | 4.10E−15 | 4.60E−14 |
| Enterococcaceae | Enterococcus | NA | 23.2109 | 4.24E−15 | 4.60E−14 |
| Lachnospiraceae | Lachnoclostridium | NA | 22.4440 | 3.30E−14 | 2.91E−13 |
| Erysipelotrichaceae | [Clostridium] innocuum group | NA | 7.1168 | 0.0003 | 0.0024 |
| Differentially abundant with antibiotics in control subjects compared to neutropenic subjects | |||||
| Lachnospiraceae | Blautia | NA | 21.1322 | 2.49E−10 | 6.95E−09 |
| Lachnospiraceae | Blautia | faecis | 8.5864 | 0.0014 | 0.0358 |
Note: The table shows species with significant fold changes in abundance with antibiotic treatment in subjects with neutropenia that did not differ or differed in the opposite direction in controls. Two additional taxa of interest were noted to be more abundant with antibiotic treatment in controls compared to neutropenic subjects (bottom). Statistical significance is defined as p < 0.05 determined by Wald test (NA = no specie(s) was associated with the sequence by ASV dataset).