Significance codes:
*** p < 0.001, ** p < 0.01, * p < 0.05, . p < 0.1

Report 4

Report 6: Univariate Log-transformed Gaussian mixed-effects models of species α-diversity across pregnancy outcome groups (A-D).

Model estimates

Family: gaussian
Formula: diversity_metric ~ pregnancy outcome group (A-D) + (1 | patient)

Data: Shannon by pregnancy outcome groups (A-D)
Number of observations: 1957; groups: PATIENT, 1547
Dispersion estimate for gaussian family (sigma^2): 0.138

Variable Estimate Std. Error z value p-value
Intercept 0.825 0.020 41.25 < 2e-16 (***)
Group B -0.034 0.032 -1.07 0.286
Group C 0.007 0.030 0.24 0.809
Group D 0.181 0.030 6.01 1.86e-09 (***)

Confidence level: 0.95
p-value adjustment: Tukey method for comparing a family of 4 estimates

Contrast Estimate SE t value p-value
A vs B 0.034 0.032 1.07 0.710
A vs C -0.007 0.030 -0.24 0.995
A vs D -0.181 0.030 -6.01 < 0.0001 (***)
B vs C -0.041 0.034 -1.23 0.610
B vs D -0.215 0.034 -6.40 < 0.0001 (***)
C vs D -0.173 0.032 -5.43 < 0.0001 (***)


Data: Phylogenetic Diversity (PD) by pregnancy outcome groups (A-D)
Family: gaussian
Number of observations: 1957; groups: PATIENT, 1547
Dispersion estimate for gaussian family (sigma^2): 0.178

Variable Estimate Std. Error z value p-value
Intercept 3.575 0.022 162.58 < 2e-16 (***)
Group B 0.045 0.035 1.28 0.200
Group C 0.145 0.033 4.36 1.31e-05 (***)
Group D 0.221 0.033 6.68 2.35e-11 (***)

Confidence level: 0.95
p-value adjustment: Tukey method for comparing a family of 4 estimates

Contrast Estimate SE t value p-value
A vs B -0.045 0.035 -1.28 0.575
A vs C -0.145 0.033 -4.36 0.0001 (***)
A vs D -0.221 0.033 -6.68 < 0.0001 (***)
B vs C -0.100 0.037 -2.72 0.0337 (*)
B vs D -0.176 0.037 -4.79 < 0.0001 (***)
C vs D -0.076 0.035 -2.17 0.133
Report 5

Report 7: Univariate Hurdle mixed-effects models (binomial and log-transformed Gaussian) assessing ARGs and MGEs detection and diversity across pregnancy outcome groups (A-D).

  1. Model estimates

Formula: diversity_metric ~ outcome_group + (1 | patient)

  • Antibiotic Resistance Genes (ARG)

    • Data: Shannon by pregnancy outcome groups (A-D)
    Part I. Family: binomial
    Number of observations: 1947, groups: PATIENT, 1547

    Variable Estimate Std. Error z value p-value
    (Intercept) 0.094 0.100 0.94 0.346
    Group B 0.038 0.161 0.24 0.811
    Group C 0.545 0.154 3.54 0.000405 (***)
    Group D 0.255 0.150 1.70 0.089 (.)

    Confidence level: 0.95
    p-value adjustment: Tukey method for comparing a family of 4 estimates.

    Contrast Odds ratio SE z value p-value
    A vs B 0.962 0.155 -0.239 0.995
    A vs C 0.580 0.089 -3.537 0.0023 (**)
    A vs D 0.775 0.116 -1.701 0.323
    B vs C 0.603 0.104 -2.939 0.0173 (*)
    B vs D 0.805 0.136 -1.284 0.573
    C vs D 1.336 0.215 1.801 0.273

    Part II. Family: gaussian
    Number of observations: 1097, groups: PATIENT, 928
    Dispersion estimate for gaussian family (sigma^2): 0.117

    Variable Estimate Std. Error z value p-value
    (Intercept) 0.560 0.028 19.86 < 2e-16 (***)
    Group B 0.098 0.045 2.20 0.028 (*)
    Group C 0.112 0.040 2.78 0.0055 (**)
    Group D 0.130 0.041 3.18 0.0015 (**)


    Confidence level: 0.95
    p-value adjustment: Tukey method for comparing a family of 4 estimates.

    Contrast Estimate SE t value p-value
    A vs B -0.098 0.045 -2.20 0.125
    A vs C -0.112 0.041 -2.78 0.0286 (*)
    A vs D -0.130 0.041 -3.18 0.0082 (**)
    B vs C -0.014 0.045 -0.31 0.990
    B vs D -0.032 0.046 -0.70 0.898
    C vs D -0.018 0.042 -0.43 0.973


    Data: Phenotypic Resistance Diversity Index (PRDI) by pregnancy outcome groups (A-D)
    Part I. Family: binomial
    Number of observations: 1947, groups: PATIENT, 1547

    Variable Estimate Std. Error z value p-value
    (Intercept) 0.094 0.100 0.94 0.346
    Group B 0.038 0.161 0.24 0.811
    Group C 0.545 0.154 3.54 0.00041 (***)
    Group D 0.255 0.150 1.70 0.089 (.)

    Confidence level: 0.95
    p-value adjustment: Tukey method for comparing a family of 4 estimates.

    Contrast Odds ratio SE z value p-value
    A vs B 0.962 0.155 -0.24 0.995
    A vs C 0.580 0.089 -3.54 0.0023 (**)
    A vs D 0.775 0.116 -1.70 0.323
    B vs C 0.603 0.104 -2.94 0.017 (*)
    B vs D 0.805 0.136 -1.28 0.573
    C vs D 1.336 0.215 1.80 0.273

    Part II. Family: gaussian
    Number of observations: 1097, groups: PATIENT, 928
    Dispersion estimate for gaussian family (sigma^2): 0.166

    Variable Estimate Std. Error z value p-value
    (Intercept) 1.130 0.029 38.33 < 2e-16 (***)
    Group B 0.135 0.047 2.86 0.0042 (**)
    Group C 0.165 0.042 3.91 9.29e-05 (***)
    Group D 0.157 0.043 3.67 0.00024 (***)

    Confidence level: 0.95
    p-value adjustment: Tukey method for comparing a family of 4 estimates.

    Contrast Estimate SE t value p-value
    A vs B -0.135 0.047 -2.86 0.022 (*)
    A vs C -0.165 0.042 -3.91 0.0006 (***)
    A vs D -0.157 0.043 -3.67 0.0014 (**)
    B vs C -0.031 0.047 -0.64 0.918
    B vs D -0.023 0.048 -0.48 0.964
    C vs D 0.008 0.043 0.18 0.998


  • Mobile Genetic Element (MGE)

    • Data: Shannon by pregnancy outcome groups (A-D)
    Part I. Family: binomial
    Number of observations: 1947, groups: PATIENT, 1547

    Variable Estimate Std. Error z value p-value Significance
    (Intercept) 0.203 0.104 1.95 0.051 (.) ·
    Group B -0.128 0.167 -0.77 0.444
    Group C 0.437 0.160 2.74 0.0062 (**) **
    Group D 0.513 0.160 3.21 0.00135 (**) **

    Confidence level: 0.95
    p-value adjustment: Tukey method for comparing a family of 4 estimates.

    Contrast Odds ratio SE z value p-value
    A vs B 1.136 0.190 0.77 0.8698
    A vs C 0.646 0.103 -2.74 0.0316 (*)
    A vs D 0.599 0.0958 -3.21 0.0074 (**)
    B vs C 0.569 0.102 -3.14 0.0091 (**)
    B vs D 0.527 0.0949 -3.56 0.0021 (**)
    C vs D 0.927 0.156 -0.45 0.969

    Part II. Family: gaussian
    Number of observations:1133, groups: PATIENT, 959
    Dispersion estimate for gaussian family (sigma^2): 0.166

    Variable Estimate Std. Error z value p-value
    (Intercept) 1.031 0.035 29.21 < 2e-16 (***)
    Group B 0.0457 0.0570 0.80 0.423
    Group C 0.119 0.0514 2.32 0.020 (*)
    Group D -0.0728 0.0506 -1.44 0.150

    Confidence level: 0.95
    p-value adjustment: Tukey method for comparing a family of 4 estimates.

    Contrast Estimate SE t value p-value
    A vs B -0.0457 0.0570 -0.80 0.854
    A vs C -0.1193 0.0514 -2.32 0.094
    A vs D 0.0728 0.0506 1.44 0.475
    B vs C -0.0736 0.0584 -1.26 0.589
    B vs D 0.1185 0.0576 2.06 0.168
    C vs D 0.1921 0.0521 3.69

    1. (**)

    GLMMs Diagnostics

    Model Diagnostic