Long-term stability of the urogenital microbiota of asymptomatic European women

Abstract

Background To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates’ identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM. Results Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5–39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found. A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1–41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance. Conclusions Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals. Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract. This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM.

Bladder Exposure to Gardnerella Activates Host Pathways Necessary for Escherichia coli Recurrent UTI

“…Importantly, these studies collected urine by catheterization or suprapubic needle aspiration to limit vaginal contamination of urine specimens, supporting the conclusion that Gardnerella can indeed be found within the bladder. In a recent longitudinal culturomics study of healthy women, Gardnerella was often present at high relative abundance in urine sample pairs collected from the same woman at different time points ( Ksiezarek et al., 2021 ). Another large study found hospital inpatients with G. vaginalis in their urine were more likely to have a history of rUTI than patients in whom G. vaginalis was not detected ( Josephson et al., 1988 ).…”

Vaginal and Anal Microbiome during Chlamydia trachomatis Infections

“…Among them, 127 OTUs were detected in vaginal and anal samples of the same subjects. Most of these OTUs were components of the female urogenital microbiota, such as Lactobacillus, Gardnerella, Streptococcus, Staphylococcus, Corynebacterium, and E. coli [17]. It is noteworthy that no significant differences in the number of OTUs shared in VS and AS were found based on the presence or absence of CT.…”

“…Among them, 127 OTUs were detected in vaginal and anal samples of the same subjects. Most of these OTUs were components of the female urogenital microbiota, such as Lactobacillus, Gardnerella, Streptococcus, Staphylococcus, Corynebacterium, and E. coli [17]. It is noteworthy that no significant In anal metagenomes (Figures 3b and S4), Enterococcus (E. faecalis and E. durans), Escherichia-Shigella, and Parasutterella were more abundant in AS−, while Desulfovibrio, Parvimonas, and Pseudomonas were more abundant in AS+.…”

Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing

“…GenBank accession numbers and species identification for FUM isolates subjected to Sanger sequencing are available in Supplementary Table S2 and previously published by Ksiezarek et al . (17). Phylogenetic analysis based on individual genes were performed to access putative novel species by using MEGA version 7.0 (21), constructed according to neighbour-joining method (22), and genetic distances were estimated using Kimura’s 2-parameter model (23).…”

“…Available studies point to dominance of e.g., Lactobacillus crispatus, Lactobacillus jensenii , and Gardnerella spp. (often mistakenly reported as Gardnerella vaginalis ) (15), and the presence of certain potential uropathogens such as Escherichia coli and Enterococcus faecalis, usually observed in low amounts (7, 13, 16, 17). In fact, detailed species-level characterization is essential to understand FUM diversity and identify key functions contributing to urinary health and disease, since specific features are often species- or even strain-specific.…”