Changes in vaginal microbiota following antimicrobial and probiotic therapy

Abstract

Background: The composition of the vaginal microbiota is known to be important for health. When infections occur, antimicrobial therapy is often poorly efficacious.

Objective and design: We used 16S rRNA gene sequencing to characterize changes in the bacterial microbiota following oral antimicrobial and probiotic interventions.

Results: While the bacterial vaginal profiles of women with vulvovaginal candidiasis were dominated by lactobacilli as in healthy women, and unchanged by therapy, Gardnerella vaginalis, Prevotella, Atopobium, Sneathia, and Megasphaera dominated the vagina of women with bacterial vaginosis (BV), and treatment with tinidazole plus Lactobacillus reuteri RC-14+L. rhamnosus GR-1 resulted in an increased relative abundance of indigenous L. iners or L. crispatus.

Conclusions: The ability to restore homeostasis provides a rationale for conjoint use of probiotics with antibiotic treatment of BV.

Keywords: Lactobacillus; bacterial vaginosis; probiotics; vulvovaginal candidiasis.

Fig. 1

Relative abundance taxa bar plot of vaginal samples from healthy asymptomatic women, and those diagnosed with BV or VVC before treatment. Taxa (groups of V6 rRNA gene sequences) are represented at the genus level where possible, with the exception of L. iners and L. crispatus, and the BV-Associated Bacteria (BVAB). The dendrogram above the bar plot represents the hierarchical average-linkage clustering of the microbiota profiles based on the computed weighted UniFrac distances.

Fig. 2

Distribution of alpha diversity within groups as measured by Shannon index. The first three box plots represent the calculated Shannon index for microbiota samples at time 0 (before treatment) in the BV, healthy, and VVC groups. After treatment (28 days), the diversities were calculated within each treatment group (probiotic and placebo) per condition (BV and VVC). The difference in diversity was compared between all pairwise groups using the Wilcoxon rank-sum test with an adjusted p-value cutoff of <0.01. Significant group differences are marked with an asterisk.

Fig. 3

Weighted UniFrac distance between pretreatment versus posttreatment samples (a) and change in principal component 1 (PC1) coordinate position (b). A weighted UniFrac distance was calculated for microbiota samples from the same individuals pre- and post-treatment (28 days) and plotted by condition and treatment group (a). In (b), the coordinate position for the first component (PC1, accounting for 67.4% of the variation) is plotted for the healthy cohort, and for the individuals in the treatment groups before and following treatment. Significantly different groups are marked with a bar and asterisk for a Bonferroni-corrected p-value <0.01 from a Wilcoxon rank-sum test.

Fig. 4

Violin plots showing change in bacterial abundance before and after treatment for BV with oral probiotic L. rhamnosus GR-1+L. reuteri RC-14 and tinidazole. The top 13 most abundant taxa across all BV samples are shown. In a violin plot, the white dot represents the median value, the black bar is the interquartile range, and the vertical width of the plot shows the density of the data along the X-axis. The left plot shows the difference in relative abundance as computed by ALDEx2. The right plot shows the difference in raw proportions for the same taxa. The reported false discovery rate (FDR) value is the result of a Benjamini–Hochberg corrected p-value from a Welch's t-test calculated within ALDEx2. Taxa with an FDR <0.05 were considered significantly different between the time points and those values are colored red. To interpret these data using L. iners as an example: the median change in proportions is approximately 25% more abundant after treatment, while the median change in clr abundance is approximately 2²=fourfold increase relative to the mean abundance of all taxa: this can also be described as L. iners becoming fourfold more abundant relative to the geometric mean abundance of all taxa following probiotic+antibiotic treatment.