TABLE 2.

DeSeq2—NonTg vs. 3xTg-AD—females. 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 compared to NonTg mice within the respective genotype.

DeSeq2—NonTg vs. 3xTg-AD—females
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)
Neurodegenerative disease related $\left(\mathit{*}\right)$
Faecalibaculum (Firmicutes)	1028.68	5.01	< 0.01	< 0.01
Bifidobacterium (Actinobacteriota)	896.02	2.45	0.01	0.10
Peptococcaceae (genus uncultured) (Firmicutes)	98.40	1.59	< 0.01	< 0.01
Putatively pro-inflammatory $\left(\mathit{**}\right)$
Parasutterella (Proteobacteria)	136.62	2.71	<0.01	0.02
Alloprevotella (Bacteroidota)	3220.18	1.78	0.02	0.12
Muribaculaceae (Bacteroidota)	14183.22	0.88	< 0.01	< 0.01
Putatively beneficial
Lachnospiraceae (NK4B4 group) (Firmicutes)	2.93	−3.69	< 0.01	0.01
Additional genera
Candidatus stoquefichus (Firmicutes)	33.26	5.58	< 0.01	< 0.01
Atopobiaceae (genus unknown) (Actinobacteriota)	78.89	3.06	< 0.01	0.02
Erysipelatoclostridium (Firmicutes)	81.09	2.98	< 0.01	< 0.01
Butyricicoccaceae UCG-009 (Firmicutes)	8.81	2.25	< 0.01	0.02
Peptococcus (Firmicutes)	3.76	2.08	0.02	0.12
Anaerotruncus (Firmicutes)	22.25	1.78	< 0.01	0.03
Anaerovoracaceae;(Eubacterium) brachy group (Firmicutes)	13.66	−1.21	< 0.01	0.03
Streptococcus (Firmicutes)	16.30	−1.83	0.03	0.14
Anaeroplasma (Firmicutes)	23.61	−1.87	0.03	0.18
Oscillospirales (genus unknown) (Firmicutes)	2.91	−2.00	0.04	0.18
Anaerofustis (Firmicutes)	0.62	−2.08	0.05	0.23
Staphylococcus (Firmicutes)	4.75	−2.94	0.01	< 0.05
Akkermansia (Verrucomicrobiota)	323.56	−3.33	< 0.01	0.02