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

α-diversity comparison across CSTs (External Dataset - ENA Number: PRJEB34536)

Report 9

Report 3: Comparison of ARG α-diversity metrics across vaginal community state types (CST) in an independent external cohort of pregnant women (PRJEB34536).

Antibiotic Resistance Genes (ARG)

Data: Shannon by CST

Kruskal-Wallis chi-squared = 15.366, df = 4, p-value = 0.003998
Pairwise comparisons using Wilcoxon rank sum test with continuity correction
p-value adjustment method: Benjamini-Hochberg (BH)

	CST I	CST II	CST III	CST IV
CST II	0.2016	-	-	-
CST III	0.0038 (**)	0.2016	-	-
CST IV	0.0080 (**)	0.3409	0.5510	-
CST V	0.2016	0.9341	0.2016	0.3464

Data: Phenotypic Resistance Diversity Index (PRDI) by CST

Kruskal-Wallis chi-squared = 40.536, df = 4, p-value = 3.352e-08
Pairwise comparisons using Wilcoxon rank sum test with continuity correction
p-value adjustment method: Benjamini-Hochberg (BH)

	CST I	CST II	CST III	CST IV
CST II	0.1845	-	-	-
CST III	1.4e-06 (***)	0.0028 (**)	-	-
CST IV	1.1e-05 (***)	0.0079 (**)	0.9621	-
CST V	0.5881	0.7065	0.0048 (**)	0.0096 (**)

Report 10

Report 4: Association between vaginal community state Type (CST) and gene detection in an independent external cohort of pregnant women (PRJEB34536).

Pearson’s Chi-squared test with Yates’ continuity correction
Chi-squared = 39.785, df = 1, p-value = 2.836e-10 (***)
P value adjustment method: BH

	CST III/IV
CST I/II/V	9.8e-11

	Absence	Presence
CST I/II/V	54	5
CST III/V	7	23