Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle

Urinary tract infections (UTIs) are among the most common bacterial infections in humans, accounting for $3.5 billion in health care expenditures yearly in the United States alone. Yet, treatments for UTI have seen little innovation over the past decade. As demonstrated in other body sites, such as the vagina and gastrointestinal (GI) tract, acute and infectious diseases often have indirect microbial contributions which serve as intriguing new targets for therapies. The recent discovery of the existence of a resident community of bacteria (i.e., microbiota) in the bladders of both women and men, represents a novel avenue for targeting UTIs. However, before targeted approaches aimed at modulating the urinary microbiota can be thoroughly investigated, it is first necessary to understand the normal modulations of these bacteria in the context of the host. Temporal dynamics in the vaginal and GI microbiota have been well described, and often linked to lifestyle factors or behaviors. Rigorous, longitudinal studies are required to study these trends. To date, few studies have assessed the urinary microbiota in such a manner -- none were comprehensive, and all were in the context of lower urinary tract symptoms. This is primarily due to the impracticality of collecting repeated transurethral catheterized urine specimens for analysis. I sought an extensive and in-depth analysis of the temporal dynamics of the lower urinary tract (LUT) microbiota in individuals without confounding urinary symptoms or disorders. Moreover, I intend to determine if any observed changes have correlations to participant-reported lifestyle factors. Through these analyses, I will aim to achieve three things. First, these data will provide the first description of the normal dynamics of the LUT microbiota. Second, our study design will serve as a framework for future research on this topic. Finally, our findings will increase our understanding of the development, risk, and prevention of UTIs by identifying patterns and potential causes of fluctuations within the LUT microbiota. In this thesis, I performed a clinical survey study as well as traditional mechanistic investigations to describe and understand the relationship between urinary microbiota dynamics and lifestyle. In the primary clinical study, I used next-generation sequencing and bacterial culture, as previously described and validated, to identify and taxonomically characterize the bacteria present in mid-stream voided urine (MSU) and peri-urethral swab specimens obtained daily from healthy, pre-menopausal women, for three months. Measures of microbiota temporal stability as well as changes in microbiota composition and alpha-diversity were obtained. I assessed for relationships between these values and various participant-reported lifestyle factors. Ultimately, I found that reporting of menstruation and sexual activity had significant impact on the microbiota of the MSU specimens in particular. The microbiota variability was observed across participants, while specific trends were very individualized but were consistent over time. I then sought to determine if the lifestyle factors were directly responsible for the observed microbiota changes. I chose to investigate sexual intercourse in particular because of the literature-documented epidemiological association with UTI risk in women. I first investigated the biological mechanism of these changes by analyzing specimens from male and female sexual partners. I determined that urinary Streptococcus isolates, which appear in elevated abundance in the MSU specimens of the female following sexual intercourse, are genomically related to isolates from the male\u27s oral flora. These data suggest that direct movement of bacteria between sexual partners results in altered female LUT microbiota following sexual intercourse. I then asked what the clinical significance of these changes were by studying the in vitro phenotypes of isolates from the normal LUT flora (i.e., Lactobacillus) as well as isolates from MSU specimens following sexual intercourse (i.e., Streptococcus). In relation to UTI risk, I found that urinary Lactobacillus isolates were bacteriostatic against strains of uropathogenic Escherichia coli (UPEC) while urinary Streptococcus isolates were not. These findings may directly relate to sexual intercourse and UTI risk, in which the normal LUT flora are protective against UTI, while the flora following sexual intercourse are not. Altogether, these data show that the LUT microbiota are dynamic and directly respond to lifestyle. Large clinical studies should be performed to further investigate the clinical significance of these findings