Characterizing the human vaginal microbiome using high-throughput sequencing

Author

Jean Megan E. Macklaim, The University of Western OntarioFollow

Degree

Doctor of Philosophy

Program

Biochemistry

Supervisor

Greg Gloor

2nd Supervisor

Gregor Reid

Joint Supervisor

Abstract

The human vaginal microbiome undoubtedly has a significant role in reproductive health and for protection from infectious organisms. Recent efforts to characterize the bacterial species of the vagina using molecular techniques have uncovered an unexpected diversity. Using high-throughput sequencing I sought to describe the structure and function of the vaginal microbiome under different physiological states including healthy, bacterial vaginosis (BV), post-menopausal vaginal atrophy, and acute vulvovaginal candidiasis (VVC).

Partial 16S rRNA gene sequencing revealed that healthy, asymptomatic women most often have vaginal biotas dominated by Lactobacillus iners or L. crispatus. In contrast, BV is a heterogeneous, highly diversified condition with reduced Lactobacillus abundance. Similar to BV, post-menopausal women experiencing vaginal dryness were depleted in lactobacilli and had a more diverse vaginal profile. In the case of VVC, the biotas were not significantly altered compared to healthy women despite the fungal overgrowth.

One organism, Lactobacillus iners was ubiquitously present in all conditions, and became predominant following antibiotic and probiotic treatment of BV. To uncover the potential role of this bacterium, I used whole genome sequencing of vaginal isolate AB-1. The genome is predicted to be the smallest of any Lactobacillus at 1.3 Mbp, but having a higher proportion of horizontally acquired genes. These results, along with predicted adhesins and a cholesterol-dependent cytolysin, indicate L. iners is highly adapted for the vagina and could have an uncharacterized role in the etiology of BV.

As BV is the most common vaginal ailment with severe implications on acquisition and

transmission of sexually transmitted infections, and complications during pregnancy, I sought iito examine the functional contribution of the organisms during BV using meta-RNA sequencing. L. iners drastically modulates gene expression in response to BV, and notably increases expression of a cholesterol-dependent cytolysin, mucin and glycerol transport and metabolic enzymes, and genes belonging to a CRISPR system - suggestive of bacteriophage influence in the community. Although diverse in taxonomic membership, there is evidence of functional conservation in BV including preference for glycogen and glycerol as carbon sources, and predicted end products of metabolism including an abundance of succinate and short-chain fatty acids. These studies add significantly to our understanding of the role lactobacilli can play in vaginal and reproductive health.

Recommended Citation

Macklaim, Jean Megan E., "Characterizing the human vaginal microbiome using high-throughput sequencing" (2013). Electronic Thesis and Dissertation Repository. 1787.
https://ir.lib.uwo.ca/etd/1787