TABLE 3.
DeSeq2—H2O vs. EtOH—females. DeSeq2 analysis. Adjusted p-values (p-value < 0.05 indicated by italics; q-value < 0.05 indicated by bold). Base mean = mean of normalized samples. Log2 FC = Log2 fold change of taxa in EtOH-fed mice compared to H2O-fed mice samples within the respective genotype.
| DeSeq2—H2O vs. EtOH—females | ||||
|---|---|---|---|---|
| Genera (phylum) | Base mean | Log2 FC EtOH over H2O | p-value | q-value |
| H2O (NonTg + 3xTg-AD, n = 20) vs. EtOH (NonTg + 3xTg-AD, n = 20) | ||||
| Alcohol consumption related | ||||
| Clostridium sensu stricto 1 (Firmicutes) | 395.40 | 2.92 | < 0.01 | 0.04 |
| Muribaculaceae (Bacteroidota) | 14183.22 | 0.87 | < 0.01 | 0.01 |
| Faecalibaculum (Firmicutes) | 1060.75 | 2.68 | 0.01 | 0.10 |
| Anaerovoracaceae (genus unknown) (Firmicutes) | 2.05 | 2.37 | 0.02 | 0.20 |
| Parasutterella (Proteobacteria) | 136.62 | 1.71 | 0.05 | 0.26 |
| Peptococcaceae (genus uncultured) (Firmicutes) | 98.40 | 0.89 | 0.03 | 0.21 |
| Bacilli RF39 (Firmicutes) | 122.82 | 0.86 | 0.04 | 0.26 |
| Enterorhabdus (Actinobacteriota) | 550.65 | 0.79 | 0.03 | 0.21 |
| Putative beneficial | ||||
| Lachnospiraceae GCA-900066575 (Firmicutes) | 76.20 | −1.35 | < 0.01 | 0.09 |
| Lachnospiraceae A2 (Firmicutes) | 105.84 | −1.70 | < 0.01 | 0.05 |
| Additional genera | ||||
| Defluviitaleaceae UCG-011 (Firmicutes) | 2.91 | 4.08 | < 0.01 | 0.01 |
| Christensenellaceae R-7 group (Firmicutes) | 5.41 | 3.03 | < 0.01 | 0.01 |
| Rhodospirillales (genus uncultured) (Proteobacteria) | 2.51 | 2.85 | 0.01 | 0.16 |
| Muribaculaceae (genus unknown) (Bacteroidota) | 102.45 | 2.72 | 0.01 | 0.12 |
| Coriobacteriaceae UCG-002 (Actinobacteriota) | 26.09 | 2.33 | 0.03 | 0.21 |
| Ruminococcaceae; (Eubacterium) siraeum group (Firmicutes) | 46.36 | 2.05 | 0.03 | 0.21 |
| Oscillospirales (genus unknown) (Firmicutes) | 2.91 | 1.91 | 0.05 | 0.26 |
| Oscillospirales UCG-010 (Firmicutes) | 17.51 | 1.45 | 0.01 | 0.16 |
| Oscillospiraceae (genus uncultured) (Firmicutes) | 235.55 | 0.68 | 0.05 | 0.26 |
| Anaerovoracaceae; (Eubacterium) nodatum group (Firmicutes) | 16.33 | −1.01 | 0.04 | 0.26 |
| Ruminococcaceae (genus unknown) (Firmicutes) | 10.74 | −1.91 | 0.03 | 0.22 |
| NonTg: H2O (n = 10) vs EtOH (n = 10) | ||||
| Alcohol consumption related | ||||
| Anaerovoracaceae (genus unclassified) (Firmicutes) | 2.05 | 2.93 | 0.03 | 0.71 |
| Putatively beneficial | ||||
| Lachnospiraceae A2 (Firmicutes) | 105.84 | −2.06 | 0.01 | 0.48 |
| Additional genera | ||||
| Clostridia UCG-014 (Firmicutes) | 406.77 | −1.17 | 0.04 | 0.71 |
| Parvibacter (Actinobacteriota) | 37.55 | −1.75 | 0.04 | 0.71 |
| Peptococcus (Firmicutes) | 3.76 | −3.49 | 0.01 | 0.48 |
| 3xTg-AD:H2O (n = 10) vs. EtOH (n = 10) | ||||
| Alcohol consumption related | ||||
| Coriobacteriaceae UCG-002 (Actinobacteriota) | 171.46 | 5.84 | < 0.01 | < 0.01 |
| Ruminococcus (Firmicutes) | 155.81 | 3.72 | < 0.01 | < 0.01 |
| Clostridium sensu stricto 1 (Firmicutes) | 395.4 | 3.70 | < 0.01 | 0.03 |
| Bacilli RF39 (Firmicutes) | 122.82 | 1.43 | 0.02 | 0.10 |
| Peptococcaceae (genus uncultured) (Firmicutes) | 98.4 | 1.27 | 0.02 | 0.13 |
| Oscillospiraceae (genus uncultured) (Firmicutes) | 235.55 | 1.25 | 0.01 | 0.06 |
| Muribaculaceae (Bacteroidota) | 14183.22 | 1.13 | < 0.01 | < 0.01 |
| Putatively beneficial | ||||
| Lachnospiraceae GCA-900066575 (Firmicutes) | 76.2 | −1.99 | < 0.01 | 0.03 |
| Additional genera | ||||
| Candidatus Saccharimonas (Patescibacteria) | 21.7 | 5.62 | < 0.01 | < 0.01 |
| Christensenellaceae R-7 group (Firmicutes) | 5.41 | 5.32 | < 0.01 | < 0.01 |
| Oscillospiraceae UCG-005 (Firmicutes) | 9.84 | 3.91 | < 0.01 | < 0.01 |
| Defluviitaleaceae UCG-011 (Firmicutes) | 2.91 | 3.52 | 0.02 | 0.10 |
| Ruminococcaceae; [Eubacterium] siraeum group (Firmicutes) | 46.36 | 3.04 | 0.02 | 0.10 |
| Muribaculaceae (genus unclassified) (Bacteroidota) | 102.45 | 2.92 | 0.04 | 0.17 |
| Monoglobus (Firmicutes) | 41.18 | 2.64 | 0.01 | 0.07 |
| Oscillospirales UCG-010 (Firmicutes) | 17.51 | 2.09 | 0.01 | 0.08 |
| Clostridia UCG-014 (Firmicutes) | 406.77 | 2.02 | < 0.01 | < 0.01 |
| Clostridia vadin BB60 group (Firmicutes) | 87.35 | 1.78 | < 0.01 | < 0.01 |
| Intestinimonas (Firmicutes) | 35.21 | −1.37 | < 0.01 | 0.03 |