The structure and diversity of strain-level variation in vaginal bacteria

The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria

Associations between the vaginal microbiome and Candida colonization in women of reproductive age

Background The composition of bacteria within the vaginal microbiome has garnered a lot of recent attention and has been associated with reproductive health and disease. Despite the common occurrence of yeast (primarily Candida) within the vaginal microbiome, there is still an incomplete picture of relationships between yeast and bacteria (especially lactobacilli), as well as how such associations are governed. Such relationships could be important to a more holistic understanding of the vaginal microbiome and its connection to reproductive health. Objective To perform molecular characterization of clinical specimens to define associations between vaginal bacteria (especially Lactobacillus species) and Candida colonization. In vitro studies were conducted to test the two most common dominant Lactobacillus species (Lactobacillus crispatus and Lactobacillus iners) in their ability to inhibit Candida growth and to examine the basis for such inhibition. Study Design A nested cross-sectional study of reproductive age women from the Contraceptive CHOICE Project was conducted. Vaginal swabs from 299 women were selected to balance race and BV status, resulting in similar representation of black and white women in each of the three Nugent score categories [normal (0-3), intermediate (4-6), and bacterial vaginosis (7-10)]. Sequencing of the 16S ribosomal gene (V4 region) was used to determine the dominant Lactobacillus species present (primarily L. iners and L. crispatus), defined as >50% of the community. Subjects without dominance by a single Lactobacillus species were classified as Diverse. A Candida-specific qPCR targeting the internally transcribed spacer 1 (ITS1) was validated using vaginal samples collected from a second cohort of women and used to assess Candida colonization. 255 nonpregnant women with sufficient bacterial biomass for analysis were included in the final analysis. Generalized linear models were employed to evaluate associations between Lactobacillus dominance, sociodemographic and risk characteristics and vaginal Candida colonization. In separate in vitro studies, the potential of cell-free supernatants from L. crispatus and L. iners cultures to inhibit Candida growth was evaluated. Results Forty-two women (16%) were vaginally colonized with Candida. Microbiomes characterized as Diverse (38%), L. iners-dominant (39%), and L. crispatus-dominant (20%) were the most common. The microbiome, race and Candida colonization co-varied with a higher prevalence of Candida among black women and L. iners-dominant communities compared to white women and L. crispatus-dominant communities. L. iners-dominant communities were more likely to harbor Candida than L. crispatus-dominant communities (OR = 2.85, 95% CI: 1.03 to 7.21; Fisher’s Exact, p = 0.048). In vitro, L. crispatus produced greater concentrations of lactic acid and exhibited significantly more pH-dependent growth inhibition of C. albicans, suggesting a potential mechanism for the clinical observations. Conclusion In nonpregnant women, L. iners-dominant communities were significantly more likely to harbor Candida than L. crispatus-dominant communities, suggesting that Lactobacillus species have different relationships with Candida. In vitro experiments indicate that L. crispatus may impede Candida colonization more effectively than L. iners through a greater production of lactic acid

Glycan cross-feeding supports mutualism between Fusobacterium and the vaginal microbiota

Women with bacterial vaginosis (BV), an imbalance of the vaginal microbiome, are more likely to be colonized by potential pathogens such as Fusobacterium nucleatum, a bacterium linked with intrauterine infection and preterm birth. However, the conditions and mechanisms supporting pathogen colonization during vaginal dysbiosis remain obscure. We demonstrate that sialidase activity, a diagnostic feature of BV, promoted F. nucleatum foraging and growth on mammalian sialoglycans, a nutrient resource that was otherwise inaccessible because of the lack of endogenous F. nucleatum sialidase. In mice with sialidase-producing vaginal microbiotas, mutant F. nucleatum unable to consume sialic acids was impaired in vaginal colonization. These experiments in mice also led to the discovery that F. nucleatum may also give back to the community by reinforcing sialidase activity, a biochemical feature of human dysbiosis. Using human vaginal bacterial communities, we show that F. nucleatum supported robust outgrowth of Gardnerella vaginalis, a major sialidase producer and one of the most abundant organisms in BV. These results illustrate that mutually beneficial relationships between vaginal bacteria support pathogen colonization and may help maintain features of dysbiosis. These findings challenge the simplistic dogma that the mere absence of healthy lactobacilli is the sole mechanism that creates a permissive environment for pathogens during vaginal dysbiosis. Given the ubiquity of F. nucleatum in the human mouth, these studies also suggest a possible mechanism underlying links between vaginal dysbiosis and oral sex

Glycan cross-feeding supports mutualism between Fusobacterium and the vaginal microbiota.

Women with bacterial vaginosis (BV), an imbalance of the vaginal microbiome, are more likely to be colonized by potential pathogens such as Fusobacterium nucleatum, a bacterium linked with intrauterine infection and preterm birth. However, the conditions and mechanisms supporting pathogen colonization during vaginal dysbiosis remain obscure. We demonstrate that sialidase activity, a diagnostic feature of BV, promoted F. nucleatum foraging and growth on mammalian sialoglycans, a nutrient resource that was otherwise inaccessible because of the lack of endogenous F. nucleatum sialidase. In mice with sialidase-producing vaginal microbiotas, mutant F. nucleatum unable to consume sialic acids was impaired in vaginal colonization. These experiments in mice also led to the discovery that F. nucleatum may also "give back" to the community by reinforcing sialidase activity, a biochemical feature of human dysbiosis. Using human vaginal bacterial communities, we show that F. nucleatum supported robust outgrowth of Gardnerella vaginalis, a major sialidase producer and one of the most abundant organisms in BV. These results illustrate that mutually beneficial relationships between vaginal bacteria support pathogen colonization and may help maintain features of dysbiosis. These findings challenge the simplistic dogma that the mere absence of "healthy" lactobacilli is the sole mechanism that creates a permissive environment for pathogens during vaginal dysbiosis. Given the ubiquity of F. nucleatum in the human mouth, these studies also suggest a possible mechanism underlying links between vaginal dysbiosis and oral sex