Int Neurourol J.  2020 Mar;24(1):41-51. 10.5213/inj.1938244.122.

The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method

Affiliations
  • 1Division of Urology, Children’s National Medical Center, George Washington University School of Medicine, Washington DC, USA
  • 2MedStar National Rehabilitation Hospital, Washington DC, USA
  • 3Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington DC, USA
  • 4Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington DC, USA
  • 5CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
  • 6Center for Genetic Medicine Research, Children’s Research Institute, Children’s National Medical Center, Washington DC, USA

Abstract

Purpose
Compared to the microbiome of other body sites, the urinary microbiome remains poorly understood. Although noninvasive voided urine specimens are convenient, contamination by urethral microbiota may confound understanding of the bladder microbiome. Herein we compared the voiding- versus catheterization-associated urine microbiome of healthy men and women.
Methods
An asymptomatic, healthy cohort of 6 women and 14 men underwent midstream urine collection, followed by sterile catheterization of the bladder after bladder refilling. Urine samples underwent urine dipstick testing and conventional microscopy and urine cultures. Samples also underwent Illumina MiSeq-based 16S ribosomal RNA gene amplification and sequencing.
Results
All organisms identified by urine culture were also identified by 16S amplification; however, next-generation sequencing (NGS) also detected bacteria not identified by cultivation. Lactobacillus and Streptococcus were the most abundant species. Abundances of the 9 predominant bacterial genera differed between the urethra and bladder. Voided and catheterized microbiomes share all dominant (>1%) genera and Operational Taxonomic Units but in similar or different proportions. Hence, urethra and bladder microbiomes do not differ in taxonomic composition, but rather in taxonomic structure. Women had higher abundance of Lactobacillus and Prevotella than men.
Conclusions
Our findings lend credence to the hypothesis that Lactobacilli are important members of the healthy urine microbiome. Our data also suggest that the microbiomes of the urethra and bladder differ from one another. In conclusion, urine collection method results in different 16S-based NGS data, likely due to the sensitivity of NGS methods enabling detection of urethral bacteria present in voided but not catheterized urine specimens.

Keyword

Microbiome; Urethra; Bladder; Microbiota; Bacteria
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