Temporal Dynamics of the Adult Female Lower Urinary Tract Microbiota

Abstract

Temporal dynamics of certain human microbiotas have been described in longitudinal studies; variability often relates to modifiable factors or behaviors. Early studies of the urinary microbiota preferentially used samples obtained by transurethral catheterization to minimize vulvovaginal microbial contributions. Whereas voided specimens are preferred for longitudinal studies, the few studies that reported longitudinal data were limited to women with lower urinary tract (LUT) symptoms, due to ease of accessing a clinical population for sampling and the impracticality and risk of collecting repeated catheterized urine specimens in a nonclinical population. Here, we studied the microbiota of the LUT of nonsymptomatic, premenopausal women using midstream voided urine (MSU) specimens to investigate relationships between microbial dynamics and personal factors. Using 16S rRNA gene sequencing and a metaculturomics method called expanded quantitative urine culture (EQUC), we characterized the microbiotas of MSU and periurethral swab specimens collected daily for approximately 3 months from a small cohort of adult women. Participants were screened for eligibility, including the ability to self-collect paired urogenital specimens prior to enrollment. In this population, we found that measures of microbial dynamics related to specific participant-reported factors, particularly menstruation and vaginal intercourse. Further investigation of the trends revealed differences in the composition and diversity of LUT microbiotas within and across participants. These data, in combination with previous studies showing relationships between the LUT microbiota and LUT symptoms, suggest that personal factors relating to the genitourinary system may be an important consideration in the etiology, prevention, and/or treatment of LUT disorders.IMPORTANCE Following the discovery of the collective human urinary microbiota, important knowledge gaps remain, including the stability and variability of this microbial niche over time. Initial urinary studies preferentially utilized samples obtained by transurethral catheterization to minimize contributions from vulvovaginal microbes. However, catheterization has the potential to alter the urinary microbiota; therefore, voided specimens are preferred for longitudinal studies. In this report, we describe microbial findings obtained by daily assessment over 3 months in a small cohort of adult women. We found that, similarly to vaginal microbiotas, lower urinary tract (LUT) microbiotas are dynamic, with changes relating to several factors, particularly menstruation and vaginal intercourse. Our study results show that LUT microbiotas are both dynamic and resilient. They also offer novel opportunities to target LUT microbiotas by preventative or therapeutic means, through risk and/or protective factor modification.

Keywords: 16S rRNA gene sequencing; lower urinary tract; menstruation; metaculturomics; microbiome; sex; urinary microbiota; urobiome.

Copyright © 2020 Price et al.

Figures

FIG 1

ProFUM clinical study design outline. Midstream voided urine (MSU) and periurethral swab specimens were self-collected daily from 8 participants from day 1 to day 74, followed by weekly collection through day 95. Daily questionnaires were completed on each of these days. The study design was divided into three phases: phase I (days 1 to 20), phase II (days 21 to 60), and phase III (days 61 to 95). During phase II, the participants were randomized (2:1) to take an oral probiotic or placebo twice daily. This assignment was performed in a double-blind manner.

FIG 2

Principal-coordinate analyses of microbiota of specimens from participants ProFUM01, ProFUM03, and ProFUM04. Analysis was done using MSU (closed circles) and periurethral (open circles) microbiota data collected from three participants indicated as follows: top left, ProFUM01; top right, ProFUM03; bottom, ProFUM04. Graphs plot the first and second principal coordinates of the data. Percentages of total variance explained by each principal coordinate are shown in parentheses.

FIG 3

Microbiota profiles of MSU specimens from all ProFUM participants. Microbiota profiles are shown as stacked bar graphs depicting the relative abundances (y axes) of various genera from MSU specimens over time in chronological order (x axes). Bars that appear white refer to days where no specimen was collected, received, or stored. A legend containing the most common genera is shown in panel J. “Other” refers to the combined relative abundances for all taxa not included in the 20 most abundant taxa. Data were generated using modified EQUC (panels A, B, C, D, E, G, and I) or 16S rRNA gene sequencing (panels F and H). *Other, used only for panels F and H.