Date of Award

Spring 5-15-2022

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Microbiology & Microbial Pathogenesis)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The vaginal environment is a dynamic ecosystem, hosting various microbial species from diverse taxa including bacteria, fungi and viruses. The composition of bacteria within the vaginal microbiome has gained a lot of recent attention and has been associated with reproductive health and disease. The vaginal microbiome of healthy reproductive-aged women is frequently dominated by Lactobacillus species and has low species diversity when compared to other anatomic sites. The composition of the bacterial community is often described in terms of five common community types. Four of the five community types are dominated by a single Lactobacillus species (L. crispatus, L. iners, L. jensenii or L. gasseri). The fifth community type is characterized by a lack of Lactobacillus dominance and often exhibits greater community diversity. While recent studies have identified associations between community type and disease, these findings have not been consistent across study populations. In light of these inconsistencies, it is important to consider other aspects of the microbial community that may explain this variance. In this dissertation, I expound on Candida colonization and bacterial strain variation and their relationships with the vaginal microbiome to provide a framework in which future studies may more holistically evaluate the microbiome and its associations with reproductive health.

Candida species frequently colonize the human vagina and colonization may lead to vulvovaginal candidiasis, a significant source of morbidity among women of reproductive age. Furthermore, recent work has suggested that Candida colonization may contribute to preterm birth. Despite this, the relationships between Candida and bacteria in the vagina are not well understood. To address this gap in knowledge, I designed a nested cohort study using vaginal swab specimens collected from nonpregnant women as part of the Contraceptive CHOICE Project. I then characterized the bacterial composition of the vaginal microbiome using 16S ribosomal profiling and determined Candida colonization status using a qPCR assay. I showed that women with L. iners-dominant microbiomes were more likely to harbor Candida than women with L. crispatus-dominant microbiomes. To identify a mechanism for this clinical observation, I evaluated the potential of cell-free supernatants from L. crispatus and L. iners cultures to inhibit Candida growth in vitro. L. crispatus produced greater concentrations of lactic acid and exhibited significantly more pH-dependent growth inhibition of C. albicans. Thus, not all Lactobacillus-dominant communities are equally associated with Candida colonization and lactic acid production may drive individual species relationships with Candida. This work provides additional evidence that L. iners-dominant communities are more permissive to vaginal colonization with potential pathogens, including Candida. As Candida correlates with bacterial community type, I conclude that the incorporation of Candida in future studies of the vaginal microbiome may lead to a better understanding of the relationships between vaginal microbiome and gynecologic health.

Strain differences in vaginal bacteria are believed to be important to reproductive disease, but little is known about the diversity, structure and evolutionary history of vaginal strains. To characterize strain variation in the vagina, I developed a metagenomic approach that utilizes core-genome SNPs to characterize strain variation in the microbiome for six commonly abundant species of bacteria: G. vaginalis, L. crispatus, L. iners, L. jensenii, L. gasseri, and A. vaginae. I showed that with the exception of L. iners, strains for all of the species cluster into multiple distinct groups. I also showed that strain diversity is lowest among Lactobacillus species. This supports the idea that Lactobacillus dominance may have evolved more recently during human evolution and that a diverse community type with abundant G. vaginalis and A. vaginae may reflect an ancestral state that is more akin to the communities found among other primates. Interestingly, I observed that species diversity is related to strain diversity within a community which indicates that the ecological forces influencing diversity may be similar at both the species and strain levels. Together this work documents a method of characterizing strain variation and provides motivation for the incorporation of strain analysis into future studies of the microbiome. If strain differences reflect functional differences that contribute to either protective or virulent phenotypes, identifying strain group associations with disease may clarify existing discrepancies in the field.


English (en)

Chair and Committee

Justin Fay

Committee Members

Justin Fay

Included in

Microbiology Commons