A systems biology approach investigating the effect of probiotics on the vaginal microbiome and host responses in a double blind, placebo-controlled clinical trial of post-menopausal women

Abstract

A lactobacilli dominated microbiota in most pre and post-menopausal women is an indicator of vaginal health. The objective of this double blinded, placebo-controlled crossover study was to evaluate in 14 post-menopausal women with an intermediate Nugent score, the effect of 3 days of vaginal administration of probiotic L. rhamnosus GR-1 and L. reuteri RC-14 (2.5×109 CFU each) on the microbiota and host response. The probiotic treatment did not result in an improved Nugent score when compared to when placebo. Analysis using 16S rRNA sequencing and metabolomics profiling revealed that the relative abundance of Lactobacillus was increased following probiotic administration as compared to placebo, which was weakly associated with an increase in lactate levels. A decrease in Atopobium was also observed. Analysis of host responses by microarray showed the probiotics had an immune-modulatory response including effects on pattern recognition receptors such as TLR2 while also affecting epithelial barrier function. This is the first study to use an interactomic approach for the study of vaginal probiotic administration in post-menopausal women. It shows that in some cases multifaceted approaches are required to detect the subtle molecular changes induced by the host to instillation of probiotic strains.

Trial registration: ClinicalTrials.gov NCT02139839.

Conflict of interest statement

Competing Interests: In order to avoid conflict of interest, all authors, including employees of Kimberly Clark, were blinded to which treatment was received by which subject, until all the sample analysis had been completed.

Figures

Figure 1. CONSORT flow diagram.

Figure 2. Microbiota heat map.

Each column represents the microbiota of a single sample with the 50 most abundant OTUs displayed with their taxonomies and the remainder pooled. Samples are clustered by the participant of origin and organized from first to last visit from left to right. The time points immediately following administration of the placebo or probiotic are indicated with a blue or green arrow (respectively). OTUs representing the putative OTUs for L. rhamnosus GR-1 and L. reuteri RC-14 have been bolded.

Figure 3. UPGMA clustering of all participants microbiota based upon weighted UniFrac distances.

In general, participants cluster most closely with themselves. The sample tips are colored by the participant of origin.

Figure 4. Selected genus relative abundances following probiotic and placebo interventions.

(A) Lactobacillus, (B) Gardnerella, (C) Atopobium, (D) Prevotella, (E) Streptococcus, (F) Staphylococcus. Following probiotic administration for 3 days, the proportion of Lactobacillus is significantly increased while that of Atopobium is decreased and Staphylococcus is increased. Placebo interventions increased Streptococcus and Staphylococcus abundance. *FDR<0.1, **FDR<0.05, ***FDR<0.01.

Figure 5. Time series of participant 17.

During the administration of probiotic between visits 6 and 7, the abundance of lactobacilli significantly increases, decreasing the proportional abundance of both Atopobium and Gardnerella. This increase is not due solely to the probiotic strains as a significant increase in indigenous L. gasseri/johnsonii takes place.