Phylotypes | PLME AICa,d | NBLME AICb,d | ZINBLME AICc,d | Best AICd | Estimate | Lower 95% CI | Upper 95% CI | Fold change | p-value | q-valuee | |
---|---|---|---|---|---|---|---|---|---|---|---|
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 |