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

Draft Genome Sequence for a Urinary Isolate of Nosocomiicoccus Ampullae

A draft genome sequence for a urinary isolate of Nosocomiicoccus ampullae (UMB0853) was investigated. The size of the genome was 1,578,043 bp, with an observed G+C content of 36.1%. Annotation revealed 10 rRNA sequences, 40 tRNA genes, and 1,532 protein-coding sequences. Genome coverage was 727× and consisted of 32 contigs, with an N50 of 109,831 bp

Genome Sequences and Annotation of Two Urinary Isolates of E. Coli

The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did not have symptoms of cystitis. Whereas strain E75 is most closely related to an avian extraintestinal pathogen, strain E78 is a member of a clade that includes extraintestinal strains often found in the human bladder. Both genomes are uncommonly rich in prophages

Draft Genome for a Urinary Isolate of Lactobacillus crispatus

While Lactobacillus crispatus contributes to the stability of normal vaginal microbiota, its role in urinary health remains unclear. As part of an on-going attempt to characterize the female urinary microbiota, we report the genome sequence of an L. crispatus strain isolated from a woman displaying no lower urinary tract symptoms

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys

The Contribution of the Female Urinary Microbiota to Lower Urinary Tract Symptoms

The recent finding that urine is not sterile raises a lot of questions: first and foremost, what microorganisms are present, and are these microorganisms correlated with clinical urinary symptoms? Recent work on the female urinary microbiota (FUM) found that the communities of microorganisms differ between women with no lower urinary tract symptoms (LUTS) and those with Urgency Urinary Incontinence (UUI) a form of over-active bladder syndrome. Specifically, a diverse or dysbiotic urinary microbiota was found to be associated with symptomatic women. This suggests the possibility that the FUM can be contributing to urinary symptoms. Conversely, it could also suggest that the FUM is simply a result of the physical environment of the urogenital tract and plays no active role in health. I hypothesize that the FUM is influencing LUTS, both as causative and preventative agents towards the clinical urinary symptoms. To test this, I first looked at the FUM of women with other urinary disorders: Stress Urinary Incontinence (SUI) and women with urinary tract infection (UTI)-like symptoms. Since many common urinary disorders share significant symptom overlap, I also assessed how the FUM correlates to individual symptoms. These data support the hypothesis that these microorganisms are able to influence LUTS. One specific organisms of the FUM, Lactobacillus crispatus, is able to exert a beneficial effect on LUTS, by inhibiting the growth and colonization of Uropathogenic Escherichia coli (UPEC), the most common cause of UTIs. The next step is to assess these potential interactions in an in vivo setting. With that collective knowledge, LUTS and UTI’s can be clinically treated with better effectiveness

Coronal Heating as Determined by the Solar Flare Frequency Distribution Obtained by Aggregating Case Studies

Flare frequency distributions represent a key approach to addressing one of the largest problems in solar and stellar physics: determining the mechanism that counter-intuitively heats coronae to temperatures that are orders of magnitude hotter than the corresponding photospheres. It is widely accepted that the magnetic field is responsible for the heating, but there are two competing mechanisms that could explain it: nanoflares or Alfv\'en waves. To date, neither can be directly observed. Nanoflares are, by definition, extremely small, but their aggregate energy release could represent a substantial heating mechanism, presuming they are sufficiently abundant. One way to test this presumption is via the flare frequency distribution, which describes how often flares of various energies occur. If the slope of the power law fitting the flare frequency distribution is above a critical threshold, $\alpha=2$ as established in prior literature, then there should be a sufficient abundance of nanoflares to explain coronal heating. We performed $>$600 case studies of solar flares, made possible by an unprecedented number of data analysts via three semesters of an undergraduate physics laboratory course. This allowed us to include two crucial, but nontrivial, analysis methods: pre-flare baseline subtraction and computation of the flare energy, which requires determining flare start and stop times. We aggregated the results of these analyses into a statistical study to determine that $\alpha = 1.63 \pm 0.03$. This is below the critical threshold, suggesting that Alfv\'en waves are an important driver of coronal heating.Comment: 1,002 authors, 14 pages, 4 figures, 3 tables, published by The Astrophysical Journal on 2023-05-09, volume 948, page 7