TABLE 4.
DeSeq2—NonTg vs. 3xTg-AD—males. DeSeq2 analysis. Taxa shown have 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 3xTg-AD mice in comparison to NonTg mice samples within the respective genotype.
| DeSeq2—NonTg vs. 3xTg-AD—males | ||||
|---|---|---|---|---|
| Genera (phylum) | Base mean | Log2 FC 3xTg-AD over NonTg | p-value | q-value |
| NonTg (H2O + EtOH, n = 20) vs. 3xTg-AD (H2O + EtOH, n = 20) | ||||
| Putative pro-inflammatory | ||||
| Parasutterella (Proteobacteria) | 136.62 | 2.58 | < 0.01 | 0.03 |
| Bacilli RF39 (Firmicutes) | 122.82 | 1.63 | < 0.01 | < 0.01 |
| Muribaculaceae (Bacteroidota) | 14183.22 | 0.74 | < 0.01 | 0.02 |
| Neurodegenerative disease related | ||||
| Bifidobacterium (Actinobacteriota) | 896.02 | 2.58 | 0.01 | 0.08 |
| Faecalibaculum (Firmicutes) | 1060.75 | 2.48 | 0.01 | 0.08 |
| Lachnospiraceae (genus uncultured) (Firmicutes) | 98.40 | 1.55 | < 0.01 | < 0.01 |
| Lachnospiraceae ASF356 (Firmicutes) | 30.24 | 1.36 | 0.01 | 0.04 |
| Putatively beneficial | ||||
| Ruminococcaceae UCG-005 (Firmicutes) | 9.84 | −1.72 | 0.02 | 0.10 |
| Lachnospiraceae FCS020 group (Firmicutes) | 21.70 | −1.05 | 0.02 | 0.10 |
| Additional genera | ||||
| Clostridia (genus unknown) (Firmicutes) | 50.94 | 2.62 | < 0.01 | <0.01 |
| Erysipelotrichaceae (Firmicutes) | 2.26 | 2.44 | 0.03 | 0.10 |
| Erysipelatoclostridium (Firmicutes) | 81.09 | 1.66 | 0.02 | 0.10 |
| Lachnoclostridium (Firmicutes) | 206.97 | −0.48 | 0.02 | 0.10 |
| Oscillibacter (Firmicutes) | 191.08 | −0.55 | 0.04 | 0.14 |
| Alistipes (Bacteroidota) | 399.22 | −0.57 | < 0.05 | 0.18 |
| Ruminococcus Incertae Sedis (Firmicutes) | 98.71 | −1.21 | < 0.01 | < 0.01 |
| Monoglobus (Firmicutes) | 41.18 | −1.73 | 0.02 | 0.10 |
| Bacteroides (Bacteroidota) | 377.55 | −1.85 | 0.02 | 0.10 |
| Streptococcus (Firmicutes) | 16.30 | −2.01 | 0.02 | 0.10 |
| Ruminococcaceae; (Eubacterium)siraeum group (Firmicutes) | 38.36 | −2.49 | 0.01 | 0.05 |
| Anaeroplasma (Firmicutes) | 23.61 | −2.56 | < 0.01 | 0.04 |
| Staphylococcus (Firmicutes) | 4.75 | −3.53 | < 0.01 | 0.02 |
| Bilophila (Desulfobacterota) | 10.21 | −3.86 | < 0.01 | 0.01 |
| Erysipelatoclostridiaceae (genus unknown) (Firmicutes) | 8.13 | −6.05 | < 0.01 | < 0.01 |