TABLE 3.
Differentially abundant amplicon sequence variant (ASV) in ileum and colon contents from male UC Davis Type 2 Diabetes Mellitus (UCD‐T2DM) rats a
| Phylum | Family | Genus | Base mean b | log2 fold difference c | p adj d | Comparison e |
|---|---|---|---|---|---|---|
| Ileum | ||||||
| Firmicutes | RF39 | RF39 | 18.5 | 6.4 | 0.02 | D1M versus ND |
| Firmicutes | Peptostreptococcaceae | Romboutsia | 1836.4 | −3.6 | <0.01 | D1M versus ND |
| Colon | ||||||
| Firmicutes | Lachnospiraceae | 116.9 | 1.9 | 0.01 | D3M versus ND | |
| Verrucomicrobiota | Akkermansiaceae | Akkermansia | 1411.1 | −5.4 | <0.01 | D3M versus ND |
| Firmicutes | Acholeplasmataceae | Anaeroplasma | 5.0 | −5.9 | 0.03 | D3M versus ND |
| Actinobacteriota | Bifidobacteriaceae | Bifidobacterium | 697.3 | 3.3 | <0.01 | D3M versus ND |
| Firmicutes | Ruminococcaceae | CAG‐352 | 118.9 | 25.5 | <0.01 | D3M versus ND |
| Firmicutes | Clostridia_vadinBB60_group | Clostridia_vadinBB60_group | 31.2 | −5.7 | 0.01 | D3M versus ND |
| Actinobacteriota | Corynebacteriaceae | Corynebacterium | 21.1 | 5.8 | 0.01 | D3M versus ND |
| Firmicutes | Erysipelotrichaceae | Dubosiella | 346.0 | 2.2 | 0.03 | D3M versus ND |
| Proteobacteria | Enterobacteriaceae | Escherichia‐Shigella | 59.3 | 4.8 | <0.01 | D3M versus ND |
| Campilobacterota | Helicobacteraceae | Helicobacter | 10.2 | −3.9 | 0.03 | D3M versus ND |
| Firmicutes | Oscillospiraceae | Intestinimonas | 61.5 | −4.2 | 0.02 | D3M versus ND |
| Firmicutes | Lachnospiraceae | Lachnospiraceae_FCS020_group | 3.2 | −5.0 | 0.04 | D3M versus ND |
| Firmicutes | Oscillospiraceae | NK4A214_group | 42.7 | 1.7 | 0.02 | D3M versus ND |
| Firmicutes | Oscillospiraceae | Oscillibacter | 118.7 | 2.6 | 0.01 | D3M versus ND |
| Firmicutes | Oscillospirales | Oscillospirales | 48.9 | 24.7 | <0.01 | D3M versus ND |
| Bacteroidota | Tannerellaceae | Parabacteroides | 13.8 | −2.4 | 0.01 | D3M versus ND |
| Firmicutes | Acidaminococcaceae | Phascolarctobacterium | 39.6 | 9.4 | <0.01 | D3M versus ND |
| Firmicutes | Ruminococcaceae | Ruminococcaceae | 2.6 | −3.6 | 0.02 | D3M versus ND |
| Firmicutes | Ruminococcaceae | Ruminococcus | 115.7 | −1.5 | 0.03 | D3M versus ND |
| Firmicutes | Erysipelotrichaceae | Turicibacter | 38.4 | 2.1 | 0.01 | D3M versus ND |
| Firmicutes | Ruminococcaceae | uncultured | 12.4 | −1.2 | 0.04 | D3M versus ND |
| Bacteroidota | Barnesiellaceae | Barnesiella | 7.9 | −3.3 | 0.04 | D1M versus ND |
| Actinobacteriota | Bifidobacteriaceae | Bifidobacterium | 697.3 | 4.2 | <0.01 | D1M versus ND |
| Firmicutes | Ruminococcaceae | CAG‐352 | 118.9 | 23.2 | <0.01 | D1M versus ND |
| Firmicutes | Clostridia_UCG‐014 | Clostridia_UCG‐014 | 109.2 | 3.1 | 0.03 | D1M versus ND |
| Firmicutes | Erysipelotrichaceae | Dubosiella | 346.0 | 2.7 | 0.03 | D1M versus ND |
| Firmicutes | RF39 | RF39 | 61.0 | 3.4 | 0.01 | D1M versus ND |
| Firmicutes | Ruminococcaceae | Ruminococcus | 115.7 | −2.7 | <0.01 | D1M versus ND |
a
UCD‐T2DM rats were non‐diabetic (ND, n = 6), had recent diabetes (2‐week post‐onset of diabetes; D1M, n = 6), or 3‐month post‐onset of diabetes (D3M, n = 6). Analysis conducted with the DESeq2 R package.
b
Normalized counts of all samples adjusting for sequencing depth.
c
Effect size estimate.
d
Bonferroni and Hochberg corrected p‐value.
e
Comparison for log twofold difference. Second listed group is the base comparison.