Longitudinal variability in the urinary microbiota of healthy premenopausal women and the relation to neighboring microbial communities: A pilot study.

Background: The understanding of longitudinal changes in the urinary microbiota of healthy women and its relation to intestinal microbiota is limited.
Methods: From a cohort of 15 premenopausal women without known urogenital disease or current symptoms, we collected catheter urine (CU), vaginal and periurethral swabs, and fecal samples on four visits over six months. Additionally, ten participants provided CU and midstream urine (MU) to assess comparability. Urine was subjected to expanded culture. 16S rRNA gene sequencing was performed on all urine, fecal, and selected vaginal and periurethral samples. Sequence reads were processed (DADA2 pipeline) and analyzed using QIIME 2 and R.
Results: Relative abundances of urinary microbiota were variable over 6-18 months. The degree of intraindividual variability of urinary microbiota was higher than that found in fecal samples. Still, nearly half of the observed beta diversity of all urine samples could be attributed to differences between volunteers (R2 = 0.48, p = 0.001). After stratification by volunteer, time since last sexual intercourse was shown to be a factor significantly contributing to beta diversity (R2 = 0.14, p = 0.001). We observed a close relatedness of urogenital microbial habitats and a clear distinction from intestinal microbiota in the overall betadiversity analysis. Microbiota compositions derived from MU differed only slightly from CU compositions. Within this analysis of low-biomass samples, we identified contaminating sequences potentially stemming from sequencing reagents.
Conclusions: Results from our longitudinal cohort study confirmed the presence of a rather variable individual urinary microbiota in premenopausal women. These findings from catheter urine complement previous observations on temporal dynamics in voided urine. The higher intraindividual variability of urinary microbiota as compared to fecal microbiota will be a challenge for future studies investigating associations with urogenital diseases and aiming at identifying pathogenic microbiota signatures.
Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: LMB has received lecture honoraria from Astellas and Merck/MSD, and travel grants from 3M and Gilead. MJGTV reports grants and personal fees from 3M, Alb Fils Kliniken GmbH, Astellas Pharma, Basilea, bioMérieux, DaVolterra, Gilead Sciences, Ferring, Glycom, Heel, MaaT Pharma, Merck/MSD, Organobalance, Pfizer, Roche Pharma, Seres Therapeutics. YK has received lecture honoraria from Merck/MSD and Gilead, and travel grants from Gilead. All remaining authors have declared no conflicts of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials.