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Table 4 Differential relative abundance of microbial phylotypes between pregnant and non-pregnant women and statistics for the phylotype level analysis

From: The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women

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

  1. aPLME: Poisson Linear Mixed Effects Model.
  2. bNBLME: Negative Binomial Linear Mixed Effects.
  3. cZINBLME: Zero-Inflated Negative Binomial Mixed-Effects Model.
  4. dAIC: Akaike Information Criterion.
  5. eq-value is p-value after adjustment for false-discovery rate (0.1).