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

Report 6

Report 8: Multivariate 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) + antibiotic treatment during pregnancy + maternal age + body mass index (BMI) + cervical cerclage + intrauterine growth restriction (IUGR) + gestational diabetes + hypertensive disorders of pregnancy + (1 | patient)

    Data: Shannon by pregnancy outcome groups (A-D)
    Number of observations: 1943; groups: PATIENT, 1533
    Dispersion estimate for gaussian family (sigma^2): 0.136

    Variable Estimate Std. Error z value Pr(>|z|)
    (Intercept) 0.675190 0.094448 7.149 8.76e-13(***)
    Group B -0.048367 0.034064 -1.420 0.155646
    Group C -0.003915 0.030601 -0.128 0.898197
    Group D 0.131271 0.033168 3.958 7.56e-05(***)
    Antibiotic (Yes) 0.053282 0.025680 2.075 0.038000(*)
    Maternal age -0.002158 0.002276 -0.948 0.343089
    BMI 0.008488 0.002242 3.786 0.000153(***)
    Cervical cerclage (Yes) 0.158989 0.048500 3.278 0.001045(**)
    IUGR (Yes) -0.006759 0.047632 -0.142 0.887162
    Gestational diabetes (Yes) -0.003931 0.030063 -0.131 0.895973
    Hypertensive disorders (Yes) 0.034643 0.067685 0.512 0.608772

    Confidence level: 0.95
    Results are averaged over the levels of antibiotic treatment during pregnancy; maternal age; BMI; cervical cerclage; IUGR; gestational diabetes; hypertensive disorders.
    p-value adjustment: Tukey method for comparing a family of 4 estimates

    contrast estimate SE df t.ratio p.value
    A vs B 0.04836675 0.03406423 1930 1.420 0.4870
    A vs C 0.00391503 0.03060054 1930 0.128 0.9993
    A vs D -0.13127106 0.03316786 1930 -3.958 0.0005 (***)
    B vs C -0.04445172 0.03570120 1930 -1.245 0.5981
    B vs D -0.17963781 0.03398566 1930 -5.286 <.0001 (***)
    C vs D -0.13518609 0.03444635 1930 -3.925 0.0005 (***)

    Data: Phylogenetic Diversity (PD) by pregnancy outcome groups (A-D)
    Family: gaussian
    Number of observations: 1943; groups: PATIENT, 1533
    Dispersion estimate for gaussian family (sigma^2): 0.178

    Variable Estimate Std. Error z value Pr(>|z|)
    (Intercept) 3.483004 0.102402 34.01 < 2e-16 (***)
    Group B 0.087636 0.037105 2.36 0.018185 (*)
    Group C 0.134720 0.033408 4.03 5.52e-05 (***)
    Group D 0.234469 0.036157 6.48 8.89e-11 (***)
    Antibiotic (Yes) -0.063485 0.027868 -2.28 0.022723 (*)
    Maternal age -0.008379 0.002467 -3.40 0.000682 (***)
    BMI 0.015266 0.002430 6.28 3.32e-10 (***)
    Cervical cerclage (Yes) 0.081353 0.052493 1.55 0.121193
    IUGR (Yes) 0.021445 0.051594 0.42 0.677659
    Gestational diabetes (Yes) 0.005456 0.032629 0.17 0.867201
    Hypertensive disorders (Yes) 0.120878 0.073219 1.65 0.098756

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

    contrast estimate SE df t.ratio p.value
    A vs B -0.08763583 0.03710515 1930 -2.362 0.0849 (.)
    A vs C -0.13472018 0.03340774 1930 -4.033 0.0003 (***)
    A vs D -0.23446873 0.03615738 1930 -6.485 <.0001 (***)
    B vs C -0.04708435 0.03881563 1930 -1.213 0.6186
    B vs D -0.14683290 0.03696010 1930 -3.973 0.0004 (***)
    C vs D -0.09974855 0.03731957 1930 -2.673
    Report 7

    Report 9: Multivariate Hurdle mixed-effects models (binomial and log-transformed Gaussian) assessing ARG and MGE detection and diversity across pregnancy outcome groups (A-D).

    Model estimates

    Formula: diversity_metric ~ outcome_group + antibiotic treatment + maternal age + body mass index (BMI) + cervical cerclage + intrauterine growth restriction (IUGR) + gestational diabetes + hypertensive disorders of pregnancy + (1 | patient)

  • Antibiotic Resistance Genes (ARG)

    • Data: Shannon by pregnancy outcome groups (A-D)
    Part I. Family: binomial
    Number of observations: 1943, groups: PATIENT, 1533

    Variable Estimate Std. Error z value p-value
    Intercept -0.348 0.483 -0.72 0.471
    Group B vs A -0.015 0.174 -0.08 0.933
    Group C vs A 0.483 0.157 3.07 0.002 (**)
    Group D vs A 0.034 0.168 0.20 0.838
    Antibiotic (Yes) 0.239 0.132 1.81 0.070 (.)
    Maternal age -0.035 0.012 -2.97 0.003 (**)
    BMI 0.061 0.012 5.04 < 1e-6 (***)
    Cervical cerclage (Yes) 0.713 0.264 2.70 0.007 (**)
    IUGR (Yes) -0.024 0.244 -0.10 0.923
    Gestational diabetes (Yes) 0.139 0.154 0.91 0.364
    Hypertensive disorders (Yes) 0.469 0.359 1.31 0.191

    Estimated marginal probability on the response scale
    Results are averaged over the levels of antibiotic treatment during pregnancy; maternal age; BMI; cervical cerclage; IUGR; gestational diabetes; hypertensive disorders.
    Confidence level: 0.95

    OUT_GROUP Probability SE 95% CI (Lower) 95% CI (Upper)
    A 0.684 0.058 0.561 0.785
    B 0.681 0.062 0.550 0.788
    C 0.778 0.045 0.677 0.854
    D 0.691 0.057 0.571 0.790

    Pairwise comparisons were adjusted using Tukey’s method
    Confidence level: 0.95

    Contrast (OUT_GROUP) Odds ratio SE z value p-value
    A vs B 1.015 0.176 0.08 0.9998
    A vs C 0.617 0.097 -3.07 0.0116 (*)
    A vs D 0.966 0.163 -0.20 0.9970
    B vs C 0.608 0.112 -2.69 0.0357 (*)
    B vs D 0.952 0.165 -0.28 0.9921
    C vs D 1.566 0.278 2.52 0.0564

    Part II. Family: gaussian
    Conditional model:
    Number of observations: 1088, groups: PATIENT, 919
    Dispersion estimate for gaussian family (sigma^2): 0.117

    Variable Estimate Std. Error z value p-value
    (Intercept) 0.464 0.124 3.75 0.00018 (***)
    Group B 0.072 0.048 1.51 0.131
    Group C 0.103 0.041 2.50 0.012 (*)
    Group D 0.096 0.046 2.09 0.037 (*)
    Antibiotic (Yes) 0.054 0.035 1.56 0.119
    Maternal age 0.00006 0.003 0.02 0.985
    BMI 0.0035 0.0029 1.21 0.225
    Cervical cerclage (Yes) -0.009 0.059 -0.15 0.879
    IUGR (Yes) 0.074 0.064 1.16 0.246
    Gestational diabetes (Yes) -0.025 0.040 -0.63 0.532
    Hypertensive disorders (Yes) 0.024 0.083 0.29 0.775

    Confidence level: 0.95
    Pairwise comparisons were adjusted using Tukey’s method:

    Contrast Estimate SE t value p-value
    A vs B -0.072 0.048 -1.51 0.432
    A vs C -0.103 0.041 -2.50 0.061 (.)
    A vs D -0.096 0.046 -2.09 0.158
    B vs C -0.031 0.048 -0.66 0.914
    B vs D -0.024 0.047 -0.51 0.956
    C vs D 0.007 0.045 0.16 0.998

    Data: Phenotypic Resistance Diversity Index (PRDI) by pregnancy outcome groups (A-D)
    Part I. Family: binomial
    Number of observations: 1943, groups: PATIENT, 1533
    Dispersion estimate for gaussian family (sigma^2): 0.167

    Variable Estimate Std. Error z value p-value
    Intercept -0.348 0.483 -0.72 0.471
    Group B -0.015 0.174 -0.08 0.933
    Group C 0.483 0.157 3.07 0.002 (**)
    Group D 0.034 0.168 0.20 0.838
    Antibiotic (Yes) 0.239 0.132 1.81 0.070 (.)
    Maternal age -0.035 0.012 -2.97 0.003 (**)
    BMI 0.061 0.012 5.04 < 1e-6 (***)
    Cervical cerclage (Yes) 0.713 0.264 2.70 0.007 (**)
    IUGR (Yes) -0.024 0.244 -0.10 0.923
    Gestational diabetes (Yes) 0.139 0.154 0.91 0.364
    Hypertensive disorders (Yes) 0.469 0.359 1.31 0.191

    Confidence level: 0.95
    Results are averaged over the levels of antibiotic treatment during pregnancy; maternal age; BMI; cervical cerclage; IUGR; gestational diabetes; hypertensive disorders.
    Pairwise comparisons were adjusted using Tukey’s method:

    Contrast (OUT_GROUP) Odds ratio SE z value p-value
    A vs B 1.015 0.176 0.08 0.9998
    A vs C 0.617 0.097 -3.07 0.0116 (*)
    A vs D 0.966 0.163 -0.20 0.9970
    B vs C 0.608 0.112 -2.69 0.0357 (*)
    B vs D 0.952 0.165 -0.28 0.9921
    C vs D 1.566 0.278 2.52 0.0564

    Part II. Family: gaussian
    Conditional model:
    Number of observations: 1088, groups: PATIENT, 919

    Variable Estimate Std. Error z value Pr(>|z|)
    (Intercept) 1.0619720 0.1300571 8.165 3.2e-16 (***)
    Group B 0.1157758 0.0501680 2.308 0.021012 (*)
    Group C 0.1595884 0.0432822 3.687 0.000227 (***)
    Group D 0.1388234 0.0482995 2.874 0.004050 (**)
    Antibiotic (Yes) 0.0400751 0.0364133 1.101 0.271087
    Maternal age -0.0007221 0.0031796 -0.227 0.820339
    BMI 0.0035036 0.0030298 1.156 0.247530
    Cervical cerclage (Yes) -0.0244801 0.0615801 -0.398 0.690975
    IUGR (Yes) 0.0480600 0.0669054 0.718 0.472556
    Gestational diabetes (Yes) -0.0215854 0.0422513 -0.511 0.609434
    Hypertensive disorders (Yes) 0.0444680 0.0868610 0.512 0.608690

    Confidence level: 0.95
    Results are averaged over the levels of antibiotic treatment during pregnancy; maternal age; BMI; cervical cerclage; IUGR; gestational diabetes; hypertensive disorders.
    Pairwise comparisons were adjusted using Tukey’s method:

    Contrast Estimate SE t value p-value
    A vs B -0.116 0.050 -2.31 0.0969 (.)
    A vs C -0.160 0.043 -3.69 0.0014 (**)
    A vs D -0.139 0.048 -2.87 0.0215 (*)
    B vs C -0.044 0.050 -0.87 0.8211
    B vs D -0.023 0.049 -0.47 0.9664
    C vs D 0.021 0.048 0.44 0.9720



  • Mobile Genetic Element (MGE)

    • Data: Shannon by pregnancy outcome groups (A-D)
    Part I. Family: binomial
    Number of observations: 1943, groups: PATIENT, 1533

    Variable Estimate Std. Error z value p-value
    Intercept -0.906 0.504 -1.80 0.072 (.)
    Group B -0.186 0.180 -1.04 0.300
    Group C 0.390 0.163 2.40 0.016
    Group D 0.281 0.176 1.59 0.111 (*)
    Antibiotic (Yes) 0.226 0.137 1.65 0.099
    Maternal age -0.014 0.012 -1.18 0.239
    BMI 0.063 0.013 5.04 < 1e-6 (***)
    Cervical cerclage (Yes) 0.837 0.283 2.96 0.003 (**)
    IUGR (Yes) -0.031 0.254 -0.12 0.904
    Gestational diabetes (Yes) -0.167 0.159 -1.05 0.293
    Hypertensive disorders (Yes) 0.144 0.363 0.40 0.692

    Estimated marginal probability on the response scale
    Confidence level: 0.95

    OUT_GROUP Probability SE Lower 95% CI Upper 95% CI
    A 0.663 0.062 0.534 0.772
    B 0.620 0.068 0.480 0.743
    C 0.744 0.051 0.632 0.831
    D 0.723 0.056 0.602 0.818

    Confidence level: 0.95
    Results are averaged over the levels of antibiotic treatment during pregnancy; maternal age; BMI; cervical cerclage; IUGR; gestational diabetes; hypertensive disorders.
    Pairwise comparisons were adjusted using Tukey’s method:

    Contrast (OUT_GROUP) Odds ratio SE z value p-value
    A vs B 1.205 0.217 1.04 0.7285
    A vs C 0.677 0.110 -2.40 0.0771 (.)
    A vs D 0.755 0.133 -1.59 0.3819
    B vs C 0.562 0.108 -3.00 0.0143 (*)
    B vs D 0.627 0.114 -2.57 0.0505 (.)
    C vs D 1.115 0.205 0.59 0.9342

    Part II. Family: gaussian
    Conditional model:
    Number of observations: 1123, groups: PATIENT, 949
    Dispersion estimate for gaussian family (sigma^2): 0.165

    Variable Estimate Std. Error z value p-value
    Intercept 1.033 0.157 6.60 < 1e-10 (***)
    Group B 0.027 0.060 0.44 0.661
    Group C 0.109 0.052 2.10 0.036 (*)
    Group D -0.095 0.057 -1.67 0.096 (.)
    Antibiotic (Yes) 0.048 0.044 1.09 0.274
    Maternal age -0.008 0.004 -2.17 0.030 (*)
    BMI 0.010 0.004 2.66 0.0078 (**)
    Cervical cerclage (Yes) -0.074 0.074 -1.00 0.316
    IUGR (Yes) -0.017 0.078 -0.22 0.823
    Gestational diabetes (Yes) 0.040 0.052 0.78 0.434
    Hypertensive disorders (Yes) 0.270 0.109 2.48 0.013 (*)

    Confidence level: 0.95
    Results are averaged over the levels of antibiotic treatment during pregnancy; maternal age; BMI; cervical cerclage; IUGR; gestational diabetes; hypertensive disorders.
    Pairwise comparisons were adjusted using Tukey’s method:

    Contrast Estimate SE t value p-value
    A vs B -0.027 0.060 -0.44 0.972
    A vs C -0.109 0.052 -2.10 0.155
    A vs D 0.095 0.057 1.67 0.342
    B vs C -0.083 0.061 -1.36 0.528
    B vs D 0.122 0.059 2.07 0.163
    C vs D 0.204 0.056 3.63

    1. (**)

    GLMMs Diagnostics

    Model Diagnostic