Table 2.
Gut Microbiome Features in Patients With COVID-19
| Gut microbiome feature | Taxon | Group | Coefficient | P value | Q value |
|---|---|---|---|---|---|
| COVID-19 (antibiotics naïve: abx−) | |||||
| Specifically enriched in COVID-19(abx−) | p_Actinobacteria|c_Actinobacteria|o_Actinomycetales|f_Actinomycetaceae|g_Actinomyces|s_Actinomyces_viscosus | COVID-19 (Abx−) | 0.243 | 8.2E-08 | 6.4E-05 |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Clostridiaceae|g_Clostridium|s_Clostridium_hathewayi | COVID-19 (Abx−) | 1.130 | 4.8E-06 | 2.5E-03 | |
| p_Bacteroidetes|c_Bacteroidia|o_Bacteroidales|f_Bacteroidaceae|g_Bacteroides|s_Bacteroides_nordii | COVID-19 (Abx−) | 0.164 | 2.3E-05 | 8.5E-03 | |
| Underrepresented in both COVID-19 and pneumonia | p_Firmicutes|c_Clostridia|o_Clostridiales|f_Eubacteriaceae|g_Eubacterium|s_Eubacterium_ventriosum | COVID-19 (Abx−) | -0.280 | 1.2E-04 | 2.5E-02 |
| COVID-19 (antibiotics exposed: abx+) | |||||
| Underrepresented in COVID-19(abx+) | p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Dorea|s_Dorea_formicigenerans | COVID-19 (Abx+) | -0.812 | 2.6E-05 | 0.00853 |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Blautia | COVID-19 (Abx+) | -0.441 | 6.1E-05 | 0.01491 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Ruminococcaceae|g_Faecalibacterium | COVID-19 (Abx+) | -0.537 | 3.2E-05 | 0.00924 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Ruminococcaceae|g_Faecalibacterium|s_Faecalibacterium_prausnitzii | COVID-19 (Abx+) | -0.537 | 3.2E-05 | 0.00924 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Eubacteriaceae | COVID-19 (Abx+) | -0.289 | 4.6E-05 | 0.01236 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Eubacteriaceae|g_Eubacterium | COVID-19 (Abx+) | -0.289 | 4.6E-05 | 0.01236 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Eubacteriaceae|g_Eubacterium|s_Eubacterium_rectale | COVID-19 (Abx+) | -0.903 | 1.7E-04 | 0.03316 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Ruminococcaceae | COVID-19 (Abx+) | -0.300 | 2.0E-04 | 0.03709 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Roseburia | COVID-19 (Abx+) | -0.598 | 2.3E-04 | 0.04018 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Coprococcus | COVID-19 (Abx+) | -0.447 | 1.6E-04 | 0.03239 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Blautia|s_Ruminococcus_obeum | COVID-19 (Abx+) | -0.623 | 4.3E-06 | 0.00243 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Lachnospiraceae_noname|s_Lachnospiraceae_bacterium_5_1_63FAA | COVID-19 (Abx+) | -0.341 | 2.5E-05 | 0.00853 | |
| Underrepresented in both COVID-19 and pneumonia | p_Firmicutes|c_Clostridia|o_Clostridiales|f_Eubacteriaceae|g_Eubacterium|s_Eubacterium_ventriosum | COVID-19 (Abx+) | -0.307 | 8.6E-06 | 0.00376 |
| Pneumonia patients | |||||
| Underrepresented in pneumonia | p_Firmicutes|c_Bacilli|o_Lactobacillales|f_Enterococcaceae|g_Enterococcus|s_Enterococcus_faecium | Pneumonia | 0.228 | 5.0E-05 | 0.01261 |
| p_Firmicutes|c_Erysipelotrichia|o_Erysipelotrichales|f_Erysipelotrichaceae|g_Erysipelotrichaceae_noname|s_Clostridium_ramosum | Pneumonia | 0.195 | 3.1E-06 | 0.00190 | |
| p_Firmicutes|c_Erysipelotrichia|o_Erysipelotrichales|f_Erysipelotrichaceae|g_Coprobacillus | Pneumonia | 0.402 | 5.2E-06 | 0.00257 | |
| p_Firmicutes|c_Clostridia|o_Clostridiales|f_Lachnospiraceae|g_Lachnospiraceae_noname|s_Lachnospiraceae_bacterium_5_1_63FAA | Pneumonia | -0.348 | 7.6E-05 | 0.01752 | |
| Underrepresented in both COVID-19 and pneumonia | p_Firmicutes|c_Clostridia|o_Clostridiales|f_Eubacteriaceae|g_Eubacterium|s_Eubacterium_ventriosum | Pneumonia | -0.256 | 3.5E-04 | 0.03539 |