Table 2.
Phylotypes differential relative abundance between pregnant women who delivered preterm and at term
| Phylotypes | PLME AIC a,d | NBLME AIC b,d | ZINBLME AIC c,d | Best AIC d | Estimate | Lower 95% CI | Upper 95% CI | Fold change | p-value | q-value e |
|---|---|---|---|---|---|---|---|---|---|---|
|
Non-significantly different phylotypes |
|
|
|
|
|
|
|
|
|
|
| Prevotella genogroup 3 |
6017.7 |
NA |
1160.3 |
ZINBLME |
2.524 |
0.341 |
4.706 |
12.5 |
0.0239 |
0.3850 |
| Dialister sp. type 2 |
3934.3 |
4142.6 |
1346.3 |
ZINBLME |
1.630 |
−0.002 |
3.261 |
5.1 |
0.0502 |
0.3850 |
| Sneathia sanguinegens |
2875.4 |
NA |
1121.2 |
ZINBLME |
1.510 |
−0.033 |
3.053 |
4.5 |
0.0550 |
0.3850 |
| Parvimonas micra |
4338.8 |
NA |
1242.3 |
ZINBLME |
1.339 |
−0.458 |
3.136 |
3.8 |
0.1422 |
0.5972 |
| Gemella |
4753.1 |
NA |
1296.3 |
ZINBLME |
1.327 |
−0.225 |
2.879 |
3.8 |
0.0927 |
0.4867 |
| BVAB2 |
12246 |
NA |
1686.4 |
ZINBLME |
1.129 |
−0.784 |
3.041 |
3.1 |
0.2440 |
0.7046 |
| Lactobacillus jensenii |
54150 |
NA |
2859 |
ZINBLME |
1.040 |
−0.518 |
2.597 |
2.8 |
0.1880 |
0.6580 |
| BVAB1 |
116789 |
NA |
2467.9 |
ZINBLME |
0.915 |
−0.976 |
2.807 |
2.5 |
0.3389 |
0.7046 |
| Megasphaera sp. type 1 |
38178 |
NA |
2860.1 |
ZINBLME |
0.717 |
−0.864 |
2.298 |
2.0 |
0.3700 |
0.7046 |
| Dialister propionicifaciens |
3433.2 |
4330.8 |
1529.3 |
ZINBLME |
0.625 |
−0.738 |
1.987 |
1.9 |
0.3648 |
0.7046 |
| Lactobacillus coleohominis |
2309.1 |
NA |
1405.6 |
ZINBLME |
0.550 |
−0.800 |
1.899 |
1.7 |
0.4206 |
0.7046 |
| Gardnerella vaginalis |
193277 |
166894 |
4311.4 |
ZINBLME |
0.520 |
−0.961 |
2.000 |
1.7 |
0.4874 |
0.7046 |
| Aerococcus christensenii |
18185 |
17841 |
2505.6 |
ZINBLME |
0.383 |
−1.107 |
1.872 |
1.5 |
0.6108 |
0.7987 |
| Atopobium vaginae |
NA |
NA |
2625.8 |
ZINBLME |
0.376 |
−1.249 |
2.001 |
1.5 |
0.6466 |
0.7987 |
| Lactobacillus crispatus |
159892 |
125388 |
3788 |
ZINBLME |
0.157 |
−1.784 |
2.098 |
1.2 |
0.8724 |
0.9068 |
| Lactobacillus iners |
263630 |
194492 |
6324.8 |
ZINBLME |
0.045 |
−0.721 |
0.811 |
1.0 |
0.9068 |
0.9068 |
| Eggerthella |
2926.9 |
NA |
1405.3 |
ZINBLME |
−0.189 |
−1.724 |
1.345 |
−1.2 |
0.8069 |
0.8918 |
| Lactobacillus vaginalis |
2682.8 |
NA |
1149.1 |
ZINBLME |
−0.293 |
−1.940 |
1.354 |
−1.3 |
0.7248 |
0.8456 |
| Ureaplasma parvum |
1866.8 |
NA |
1184.9 |
ZINBLME |
−0.374 |
−1.480 |
0.732 |
−1.5 |
0.5033 |
0.7046 |
| Atopobium rimae |
1386.9 |
NA |
883.8 |
ZINBLME |
−0.522 |
−1.910 |
0.865 |
−1.7 |
0.4567 |
0.7046 |
| Lactobacillus gasseri | 34741 | NA | 1592.4 | ZINBLME | −0.864 | −2.847 | 1.118 | −2.4 | 0.3887 | 0.7046 |
aPLME: Poisson Linear Mixed Effects Model.
bNBLME: Negative Binomial Linear Mixed Effects.
cZINBLME: Zero-Inflated Negative Binomial Mixed-Effects Model.
dAIC: Akaike Information Criterion.
eq-value is p-value after adjustment for false-discovery rate (0.1).