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

α-diversity comparison across CSTs (InSPIRe cohort)

Report 1

Report 1: Comparison of species, ARG and MGE α-diversity metrics across vaginal community state types (CST).

  • Species

    • Data: Shannon by CST
    Kruskal-Wallis chi-squared = 380.66, df = 4, p-value < 2.2e-16 (***)
    Pairwise comparisons using Dunn’s test
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II < 2e-16 (***) - - -
    CST III < 2e-16 (***) < 2e-16 (***) - -
    CST IV < 2e-16 (***) 0.2205 < 2e-16 (***) -
    CST V < 2e-16 (***) 0.2532 < 2e-16 (***) 0.0756

    Data: Phylogenetic diversity (PD) by CST
    Kruskal-Wallis chi-squared = 86.01, df = 4, p-value < 2.2e-16 (***)
    Pairwise comparisons using Dunn’s test
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II 0.0056 (**) - - -
    CST III < 2e-16 (***) 0.4832 - -
    CST IV < 2e-16 (***) 0.0018 (**) < 2e-16 (***) -
    CST V 0.0359 (*) 0.3995 0.3984 0.0016


  • Antibiotic Resistance Genes (ARG)

    • Data: Shannon by CST
    Kruskal–Wallis chi-squared = 196.57, df = 4, p-value < 2.2e-16 (***)
    Pairwise comparisons using Dunn’s test
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II 0.0046 (**) – – –
    CST III < 2e-16 (***) < 2e-16 (***) – –
    CST IV < 2e-16 (***) 0.0002 (**) 0.0400 (***) –
    CST V 0.0100 (*) 0.4964 < 2e-16 (***) 0.0007 (***)

    Data: Phenotypic Resistance Diversity Index (PRDI) by CST
    Kruskal–Wallis chi-squared = 341.45, df = 4, p-value < 2.2e-16
    Pairwise comparisons using Dunn’s test
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II 0.0001 (***) – – –
    CST III < 2e-16 (***) < 2e-16 (***) – –
    CST IV < 2e-16 (***) < 2e-16 (***) 0.0033 (**) –
    CST V 0.0016 (**) 0.3829 < 2e-16 (***) < 2e-16 (***)


  • Mobile Genetic Element (MGE)

    • Data: Shannon by CST
    Kruskal–Wallis chi-squared = 281.99, df = 4, p-value < 2.2e-16 (***)
    Pairwise comparisons using Dunn’s test
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II 0.1485 – – –
    CST III < 2e-16 (***) < 2e-16 (***) – –
    CST IV < 2e-16 (***) 0.0002 (***) < 2e-16 (***) –
    CST V 0.0135 (*) 0.1358 < 2e-16 (***) 0.0319 (*)
    Report 2

    Report 2: Association between vaginal community state Type (CST) and gene detection.

  • Antibiotic Resistance Genes (ARG)

    • Pearson’s Chi-squared test
    chi-squared = 593.01, df = 4, p-value < 2.2e-16 (***)
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II 2.8e-10 (***) - - -
    CST III < 2e-16 (***) < 2e-16 (***) - -
    CST IV < 2e-16 (***) 1.2e-06 (***) 3.3e-09 (***) -
    CST V 1.2e-06 (***) 0.61 < 2e-16 (***) 1.2e-06 (***)
    CST Type Absence Presence
    CST I 566 184
    CST II 70 76
    CST III 55 454
    CST IV 115 332
    CST V 54 51


  • Mobile Genetic Element (MGE)

    • Pearson’s Chi-squared test
    chi-squared = 263.96, df = 4, p-value < 2.2e-16 (***)
    p-value adjustment method: Benjamini-Hochberg (BH)

    CST I CST II CST III CST IV
    CST II 9.8e-07 (***) - - -
    CST III < 2e-16 (***) 0.00024 (***) - -
    CST IV < 2e-16 (***) 0.00105 (**) 0.65207 -
    CST V 0.04029 (*) 0.08014 (.) 8.4e-08 (***) 6.0e-07 (***)
    CST Absence Presence
    CST I 475 275
    CST II 59 87
    CST III 122 387
    CST IV 113 334
    CST V 55 50