Fig. 2

Quantitative PCR of bacterial 16S rRNA gene abundance in expanded study samples and blank controls. Quantitative PCR was performed on DNA extracts from blank controls (Blk = 53), placenta (Plac; N = 60), vagino-rectal swabs (VRS; N = 28), cord blood (Crd bld; N = 28), and maternal blood (Mat bld; N = 28) from the expanded study. a CT value represented for individual samples from the various sites including blanks. Undetermined and/or low confidence Cq CT values, i.e., below the limit of reliable detection (CT > 35), are plotted with hypothetical value of 40. b Box plot of estimated 16S rRNA gene copy number for samples with CT values less than 35, including placenta (Plac; N = 31 of 60 total samples), vagino-rectal swabs (VRS; N = 27/28), cord blood (Crd bld; N = 14/28), and maternal blood (Mat bld; N = 25/28) from the expanded study. Undetermined and/or low confidence Cq CT values, i.e., below the limit of reliable detection (CT > 35), for some samples and all 53 blanks contributed to discrepancy in the frequency of samples plotted as well as omission of blanks from the plot. VRS were significantly (*** ρ < 0.0001) different from Plac, Crd_Bld, and Mat_Bld (ANOVA followed by Tukey’s test). However, placenta, cord blood, and maternal blood samples were not significantly different (ρ = 1)