Abstract
The endometrial cavity is an upper genital tract site previously thought as sterile, however, advances in culture-independent, next-generation sequencing technology have revealed that this low-biomass site harbors a rich microbial community which includes multiple Lactobacillus species. These bacteria are considered to be the most abundant non-pathogenic genital tract commensals. Next-generation sequencing of the female lower genital tract has revealed significant variation amongst microbial community composition with respect to Lactobacillus sp. in samples collected from healthy women and women with urogenital conditions. The aim of this study was to evaluate our ability to characterize members of the genital tract microbial community to species-level taxonomy using variable regions of the 16S rRNA gene. Samples were interrogated for the presence of microbial DNA using next-generation sequencing technology that targets the V5–V8 regions of the 16S rRNA gene and compared to speciation using qPCR. We also performed re-analysis of published data using alternate variable regions of the 16S rRNA gene. In this analysis, we explore next-generation sequencing of clinical genital tract isolates as a method for high throughput identification to species-level of key Lactobacillus sp. Data revealed that characterization of genital tract taxa is hindered by a lack of a consensus protocol and 16S rRNA gene region target allowing comparison between studies.
Highlights
Molecular microbiology techniques have changed our ability to identify microbial communities, revolutionizing the way we assess female genital tract microbiomes
In order to determine the Lactobacillus species present in upper genital tract (UGT) clinical samples (Table 1), 16S rRNA gene sequencing was performed on the V5-V8 variable region
Ten operational taxonomic units (OTUs) identified in the genital tract were attributable to Lactobacillus sp. [Lactobacillus sp. genus level (n = 2), L. crispatus (n = 2), L. iners (n = 3), L. intestinalis (n = 1), L. jensenii (n = 1), and L. vaginalis (n = 1)]
Summary
Molecular microbiology techniques have changed our ability to identify microbial communities, revolutionizing the way we assess female genital tract microbiomes. The discovery that lactobacilli do not dominate the lower or upper genital tract of all healthy women and are present in both health and disease suggests that there is redundancy in function and protection based on community membership; and all lactobacilli may not provide the same level of protection in the genital tract environment. The objective of this study was to examine the discriminatory power of molecular microbiology techniques that exploit the conserved 16S rRNA gene for identification of genital tract lactobacilli. To achieve this goal, the analysis was completed with re-analyzed published data and work in our laboratory
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