Exploring the Diversity of Gardnerella vaginalis in the Genitourinary Tract Microbiota of Monogamous Couples Through Subtle Nucleotide Variation

Abstract

BackgroundBacterial vaginosis (BV) is an enigmatic disease of unknown origin that affects a large percentage of women. The vaginal microbiota of women with BV is associated with serious sequelae, including abnormal pregnancies. The etiology of BV is not fully understood, however, it has been suggested that it is transmissible, and that G. vaginalis may be an etiological agent. Studies using enzymatic assays to define G. vaginalis biotypes, as well as more recent genomic comparisons of G. vaginalis isolates from symptomatic and asymptomatic women, suggest that particular G. vaginalis strains may play a key role in the pathogenesis of BV.Methodology/Principal FindingsTo explore G. vaginalis diversity, distribution and sexual transmission, we developed a Shannon entropy-based method to analyze low-level sequence variation in 65,710 G. vaginalis 16S rRNA gene segments that were PCR-amplified from vaginal samples of 53 monogamous women and from urethral and penile skin samples of their male partners. We observed a high degree of low-level diversity among G. vaginalis sequences with a total of 46 unique sequence variants (oligotypes), and also found strong correlations of these oligotypes between sexual partners. Even though Gram stain-defined normal and some Gram stain-defined intermediate oligotype profiles clustered together in UniFrac analysis, no single G. vaginalis oligotype was found to be specific to BV or normal vaginal samples.ConclusionsThis study describes a novel method for investigating G. vaginalis diversity at a low level of taxonomic discrimination. The findings support cultivation-based studies that indicate sexual partners harbor the same strains of G. vaginalis. This study also highlights the fact that a few, reproducible nucleotide variations within the 16S rRNA gene can reveal clinical or epidemiological associations that would be missed by genus-level or species-level categorization of 16S rRNA data.

Host-specificity among abundant and rare taxa in the sponge microbiome

“…The oligotyping computational method (Eren et al, 2011(Eren et al, , 2013a further explored potential host-specificity patterns using subtle nucleotide variation in closely related Hexadella microbiota. From the entire data set, we submitted 2 112 927 high-quality Illumina V6 fragments that GAST identified as Nitrospira to the oligotyping pipeline version 0.6 (available from http://oligotyping.org).…”

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

“…Bacterial communities were analyzed using 454 pyrosequencing of the V6V4 region of the bacterial 16S rRNA gene. Dates of sampling, specific water depth and locations are given in Table 1. virulent and nonpathogenic microorganisms (Eren et al, 2011), host-specific fecal-indicator bacteria (McLellan et al, 2013), marine SAR11 oligotypes and host-specificity in spongehosted microbial communities (Reveillaud et al, 2014). Importantly, the method is immune to complications originating from the occurrence of multiple copies of the 16S rRNA gene.…”

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

“…The vaginal microbial community may depend on the number of sexually active individuals (that is, mating partners) in a group. For example, microbial communities and strains are shared between mating partners (Jaspers and Overmann, 2004;Marrazzo et al, 2009;Danielsson et al, 2011;Eren et al, 2011) and sexual activity is a strong risk factor for dysbiosis (Fethers et al, 2008). In humans, microbial ecologies vary considerably between women depending on their mating group size, and BV is most common in women who have new or multiple sexual partners (Fethers et al, 2008(Fethers et al, , 2009Eren et al, 2011).…”