Table 1. The percent compositions of microbiomes at the levels of class, order, and family in wild-type and Tg-APP/PS1 mice.
| Phylum | Clas | Order | Family | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Taxon | Occupancy (%; Mean) | z-score | Taxon | Occupancy (%; Mean) | z-score | Taxon | Occupancy (%; Mean) | z-score | Taxon | Occupancy (%; Mean) | z-score | ||||
| WT | Tg | WT | Tg | WT | Tg | WT | Tg | ||||||||
| Firmicutes | 34.7 | 57.5 | ↑ 3.4 | Clostridia | 18.1 | 25.9 | ↑ 1.4 | Clostridiales | 18.1 | 25.9 | ↑ 1.4 | *Unidentified | 4.7 | 7 | ↑ 1.1 |
| Lachnospiraceae | 3.1 | 5.9 | ↑ 1.5 | ||||||||||||
| [Mogibacteriaceae] | 0 | 0.1 | ↑ << | ||||||||||||
| Eubacteriaceae | 0 | 0.1 | ↑ << | ||||||||||||
| Bacilli | 16 | 30.3 | ↑ 5.4 | Lactobacillales | 8.3 | 17 | ↑ 3.2 | Lactobacillaceae | 5.7 | 3.1 | ↓ −1.7 | ||||
| Aerococcaceae | 0.6 | 11.1 | ↑ 10.6 | ||||||||||||
| Leuconostocaceae | 0 | 0.3 | ↑ 4.2 | ||||||||||||
| Bacillales | 7.3 | 12.9 | ↑ 1.1 | Staphylococcaceae | 6.4 | 12 | ↑ 1 | ||||||||
| Other | 0 | 0.3 | ↑ 27.8 | Other | 0 | 0.3 | ↑ 27.8 | ||||||||
| Proteobacteria | 30.5 | 20.7 | ↓ −1.6 | Gammaproteobacteria | 14.4 | 13 | Pseudomonadales | 9.1 | 8.8 | Pseudomonadaceae | 3.1 | 4.5 | ↑ 1.4 | ||
| Xanthomonadales | 0 | 0.1 | ↑ 5.6 | Xanthomonadaceae | 0 | 0.1 | ↑ 5.6 | ||||||||
| Alphaproteobacteria | 10.2 | 3.7 | Sphingomonadales | 3.8 | 0.7 | ↓ −1.1 | Sphingomonadaceae | 3.8 | 0.7 | ↓ −1.1 | |||||
| Rhizobiales | 1 | 1.4 | Bartonellaceae | 0 | 0.1 | ↑ << | |||||||||
| Caulobacterales | 0.2 | 0.9 | ↑ 2.1 | Caulobacteraceae | 0.2 | 0.9 | ↑ 2.1 | ||||||||
| Betaproteobacteria | 4.7 | 3.4 | Burkholderiales | 4.2 | 3.2 | Comamonadaceae | 2.5 | 1.1 | ↓ −1.1 | ||||||
| Rhodocyclales | 0.2 | 0 | ↓ >> | Rhodocyclaceae | 0.2 | 0 | ↓ >> | ||||||||
| Bacteroidetes | 17.8 | 8.7 | Bacteroidia | 17.5 | 7.9 | Bacteroidales | 17.5 | 7.9 | S24-7 | 6.3 | 1.8 | ↓ −1 | |||
| [Odoribacteraceae] | 0 | 0.1 | ↑ << | ||||||||||||
| Flavobacteriia | 0.3 | 0.3 | Flavobacteriales | 0.3 | 0.3 | Flavobacteriaceae | 0.2 | 0 | ↓ >> | ||||||
| Cytophagia | 0 | 0.2 | ↑ << | Cytophagales | 0 | 0.2 | ↑ << | Cytophagaceae | 0 | 0.2 | ↑ << | ||||
| Sphingobacteriia | 0 | 0.2 | ↑ 2.6 | Sphingobacteriales | 0 | 0.2 | ↑ 2.6 | Sphingobacteriaceae | 0 | 0.2 | ↑ 2.6 | ||||
| Actinobacteria | 7.7 | 5.2 | Actinobacteria | 6.9 | 4.3 | Actinomycetales | 6.1 | 3.3 | Corynebacteriaceae | 3.5 | 0.9 | ↓ −1.4 | |||
| Micrococcaceae | 0 | 0.1 | ↑ << | ||||||||||||
| Nocardioidaceae | 0 | 0.1 | ↑ 6.2 | ||||||||||||
| TM7 | 3.8 | 2.6 | TM7-3 | 3.8 | 2.6 | *Unidentified | 0 | 0.2 | ↑ << | *Unidentified | 0 | 0.2 | ↑ << | ||
| Tenericutes | 0.9 | 0.3 | ↓ −1.1 | Mollicutes | 0.9 | 0.3 | ↓ −1.1 | RF39 | 0.9 | 0.3 | ↓ −1.1 | *Unidentified | 0.9 | 0.3 | ↓ −1.1 |
| Cyanobacteria | 0.9 | 0.5 | 4C0d-2 | 0 | 0.2 | ↑ 1.4 | YS2 | 0 | 0.2 | ↑ 1.4 | *Unidentified | 0 | 0.2 | ↑ 1.4 | |
| Gemmatimonadetes | 0.2 | 0 | Gemmatimonadetes | 0.2 | 0 | ↓ >> | Gemmatimonadales | 0.1 | 0 | ↓ >> | *Unidentified | 0.1 | 0 | ↓ >> | |
| *Unidentified | 0.1 | 0 | ↓ >> | *Unidentified | 0.1 | 0 | ↓ >> | ||||||||
| [Thermi] | 0 | 0.2 | ↑ << | Deinococci | 0 | 0.2 | ↑ << | Deinococcales | 0 | 0.2 | ↑ << | Deinococcaceae | 0 | 0.2 | ↑ << |
| Fibrobacteres | 0 | 0.1 | ↑ << | TG3 | 0 | 0.1 | ↑ << | TG3-1 | 0 | 0.1 | ↑ << | TSCOR003-O20 | 0 | 0.1 | ↑ << |
| Summation | 96.5 | 95.6 | 93.1 | 92.6 | 77.3 | 83.9 | 41.5 | 51.8 | |||||||
The family members of microbiomes for which occupancy differed by more than one standard deviation (SD; one z) in Tg-APP/PS1 mice from that of wild-type mice are presented, along with the higher taxonomy levels. Those occupying 0.1% and higher in either wild-type or Tg-APP/PS1 mice were included.
Data are presented as the mean percentages and z-scores. The z-score is X − µ/σ, where µ=mean; X=individual score; σ=standard deviation (SD). Increases and decreases in the mean occupancy by more than one z in Tg-APP/PS1 are indicated by ↑ and ↓, respectively. « and » denote infinite increases and decreases, respectively.
1)APPswe/PSEN1dE9; 2)APPswe/PSEN1-L166P