Table 4.
Differential relative abundance of microbial phylotypes between pregnant and non-pregnant women and statistics for the phylotype level analysis
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
|
Phylotypes less abundant in pregnancy | |||||||||||
| |
Clostridiales Family XI Incertae Sedis |
3488.3 |
2996.9 |
2998.9 |
NBLME |
-7.095 |
-9.020 |
-5.169 |
-1205.6 |
0.0001 |
0.0002 |
| |
Anaerococcus vaginalis |
3043.8 |
2748.2 |
2759.9 |
NBLME |
-5.873 |
-7.260 |
-4.486 |
-355.4 |
0.0001 |
0.0002 |
| |
Anaerococcus |
5252.6 |
3804.3 |
3806.3 |
NBLME |
-5.557 |
-6.605 |
-4.509 |
-259.0 |
0.0001 |
0.0002 |
| |
Prevotella genogroup 2 |
5510.3 |
4498.2 |
4504.2 |
NBLME |
-5.019 |
-5.655 |
-4.384 |
-151.3 |
0.0001 |
0.0002 |
| |
Peptoniphilus |
4707.8 |
4431.3 |
4433.3 |
NBLME |
-4.921 |
-5.670 |
-4.171 |
-137.1 |
0.0001 |
0.0002 |
| |
Streptococcus anginosus |
3285.4 |
2565.8 |
2583.8 |
NBLME |
-4.629 |
-5.748 |
-3.511 |
-102.4 |
0.0001 |
0.0002 |
| |
Actinomycetales |
5672.8 |
5110.1 |
5112.1 |
NBLME |
-4.546 |
-5.281 |
-3.811 |
-94.2 |
0.0001 |
0.0002 |
| |
Leptotrichia amnionii |
7299.3 |
3889.1 |
3893.3 |
NBLME |
-4.490 |
-5.359 |
-3.621 |
-89.1 |
0.0001 |
0.0002 |
| |
Finegoldia magna |
4687.1 |
4300.6 |
4302.6 |
NBLME |
-4.174 |
-4.958 |
-3.391 |
-65.0 |
0.0001 |
0.0002 |
| |
Prevotella |
4540 |
4094.7 |
4096.7 |
NBLME |
-3.870 |
-4.502 |
-3.238 |
-48.0 |
0.0001 |
0.0002 |
| |
Clostridiales |
5864.5 |
4852.6 |
NA |
NBLME |
-3.373 |
-4.274 |
-2.472 |
-29.2 |
0.0001 |
0.0002 |
| |
Atopobium |
3853.1 |
3275 |
3261.6 |
ZINBLME |
-3.268 |
-3.943 |
-2.593 |
-26.3 |
0.0001 |
0.0002 |
| |
Bacteria |
3167.5 |
3033 |
3040.1 |
NBLME |
-3.083 |
-3.921 |
-2.245 |
-21.8 |
0.0001 |
0.0002 |
| |
Prevotella.bivia |
4178.9 |
3043 |
3045 |
NBLME |
-3.038 |
-4.089 |
-1.986 |
-20.9 |
0.0001 |
0.0002 |
| |
Eggerthella |
3149.7 |
3083.7 |
3065.2 |
ZINBLME |
-1.936 |
-2.813 |
-1.060 |
-6.9 |
0.0001 |
0.0002 |
| |
Gardnerella vaginalis |
5472 |
5105.1 |
5076.7 |
ZINBLME |
-1.760 |
-2.253 |
-1.266 |
-5.8 |
0.0001 |
0.0002 |
| |
Dialister |
4048.5 |
3939.6 |
3940.9 |
NBLME |
-1.399 |
-2.147 |
-0.651 |
-4.1 |
0.0003 |
0.0004 |
| |
Ureaplasma |
2819 |
2700.6 |
2707.8 |
NBLME |
-1.153 |
-1.817 |
-0.490 |
-3.2 |
0.0007 |
0.0010 |
| |
Lactobacillus |
10572 |
9170.2 |
9172.2 |
NBLME |
-0.726 |
-1.169 |
-0.283 |
-2.1 |
0.0013 |
0.0017 |
| |
Atopobium vaginae |
12734 |
6971.9 |
7024.5 |
PLME |
-2.381 |
-3.946 |
-0.816 |
-10.8 |
0.0029 |
0.0037 |
| |
Parvimonas micra |
4512.2 |
3835.1 |
3821.7 |
ZINBLME |
-4.202 |
-7.609 |
-0.795 |
-66.8 |
0.0157 |
0.0183 |
| |
Bifidobacteriaceae |
4056.8 |
3989.9 |
3991.9 |
NBLME |
-0.660 |
-1.429 |
0.110 |
-1.9 |
0.0927 |
0.0998 |
|
Phylotypes more abundant in pregnancy | |||||||||||
| |
Lactobacillus vaginalis |
2489.2 |
2467.9 |
2458.2 |
ZINBLME |
1.704 |
1.190 |
2.218 |
5.5 |
0.0001 |
0.0002 |
| |
Lactobacillus jensenii |
6544.1 |
5564.1 |
5549.7 |
ZINBLME |
1.549 |
1.453 |
1.645 |
4.7 |
0.0001 |
0.0002 |
| |
Lactobacillus crispatus |
11702 |
8094 |
8263.2 |
NBLME |
0.754 |
0.212 |
1.295 |
2.1 |
0.0064 |
0.0078 |
| |
Lactobacillus gasseri |
6917.3 |
4412.4 |
NA |
NBLME |
1.193 |
0.214 |
2.172 |
3.3 |
0.0170 |
0.0190 |
|
Non-significantly different phylotypes | |||||||||||
| |
Lactobacillus iners |
18755 |
12576 |
12604 |
NBLME |
0.165 |
-0.136 |
0.466 |
1.2 |
0.2824 |
0.2929 |
| Aerococcus christensenii | 4321.2 | 3986.9 | 3957.1 | ZINBLME | -0.425 | -1.251 | 0.401 | -1.5 | 0.3132 | 0.3132 | |
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).