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

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.

Conclusion: 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.

Keywords: Bacteria; Bladder; Microbiome; Microbiota; Urethra.

Fig. 1.

Microbiome of voided versus catheterized urine samples from 20 asymptomatic adults. Comparison of the most common genera present by 16s ribosomal RNA sequencing across all samples. Participants are cohorted by sex (females and males) and presented by increasing age. Paired samples are combined by brackets (1st column, catheterized sample; 2nd column, voided sample).

Fig. 2.

Alpha-diversity box plots for voided versus catheterized urine samples and male versus female samples. ACE, abundance-based coverage estimator; PD, phylogenetic diversity; OTU, Operational Taxonomic Unit.

Fig. 3.

PCoAs plots for voided and catheterized urine samples and male and female samples using weighted (A) and unweighted (B) Unifrac distances. PCoA, principal coordinates analysis; Void, voiding-associated urine microbiome; Cath, catheterization-associated urine microbiome.

Fig. 4.

Prevalent genera identified by 16S sequencing of voided (orange) and catheterized (blue) urine samples in an asymptomatic female (A) and male (B).