Commentary on “The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method”

Article information

Int Neurourol J. 2020;24(2):182-184
Publication date (electronic) : 2020 June 30
doi :
Department of Urology, St. Vincent’s Hospital, The Catholic University of Korea, Suwon, Korea
Corresponding author: Seung-Ju Lee Department of Urology, St. Vincent’s Hospital, The Catholic University of Korea, 93 Jungbu-daero, Paldal-gu, Suwon 16247, Korea E-mail:
Received 2020 May 14; Accepted 2020 May 19.

To the editor,

I read with great interest the article titled “The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method” published by Pohl et al. in the International Neurourology Journal in March 2020 [1]. The authors concluded that the urinary microbiome differed according to urine collection methods and that sex differences in the core microbiome exist.

When I analyzed articles that studied urinary microbiome in healthy individuals, or healthy controls in case-control studies, most studies showed similar results (Table 1). Lactobacillus was the predominant genus in the urinary microbiome in females, whereas a more heterogeneous group of microbiomes was shown in males [2-23]. The study by Wolfe et al. [5] was the only study that compared different urine collection methods, and they concluded that the best methods are suprapubic aspiration and transurethral catheterization.

Articles that studied the urinary microbiome in healthy individuals, or healthy controls in case-control studies

There are still clear limitations in the study of the human urinary microbiome. Due to the heterogeneous design of urinary microbiome studies, it is difficult to make comparisons between studies and to draw conclusions. There are differences according to the urine collection method, 16s rRNA analysis tools, statistical methods, and the taxonomic database on which the reporting of genera or species is based. These heterogeneous study designs cause discrepancies in results. In addition, as the authors clearly pointed out, many other factors can influence the urinary microbiome, such as age, sex, dietary habits, infections and antimicrobial use, hormonal status, and regional variation.

Several points should be considered in future studies involving the urinary microbiome. First, a larger sample size is needed. Second, standardization of methodology and reporting is necessary to facilitate comparisons between studies. Third, more studies on the normal urinary microbiome and factors influencing its composition are needed. Age, sex, and urine collection methods are known factors, but many other factors likely exist. One point to consider in this regard is that it may be impossible to define a “universal norm” regarding the urinary microbiome. Rather than defining a universal norm, identifying the normal urinary microbiome in each individual and using it as a personalized reference for future disease may be a more reasonable approach. Fourth, the connection between dysbiosis and disease should be more clearly identified. When this connection is found, it may become possible to use the urinary microbiome in diagnosis or treatment. Lastly, studies have suggested that the overall composition and richness of the microbiota play an important role in modulating vaccine response [24]. In this regard, the effects of the urinary microbiome on vaccinations for urinary tract infection may be an interesting topic for future studies.


Conflict of Interest

No potential conflict of interest relevant to this article was reported.


1. Pohl HG, Groah SL, Perez-Losada M, Ljungberg I, Sprague BM, Chandal N, et al. The urine microbiome of healthy men and women differs by urine collection method. Int Neurourol J 2020;24:41–51.
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4. Nelson DE, Dong Q, Van der Pol B, Toh E, Fan B, Katz BP, et al. Bacterial communities of the coronal sulcus and distal urethra of adolescent males. PLoS One 2012;7e36298.
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10. Thomas-White KJ, Hilt EE, Fok C, Pearce MM, Mueller ER, Kliethermes S, et al. Incontinence medication response relates to the female urinary microbiota. Int Urogynecol J 2016;27:723–33.
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14. Wang H, Altemus J, Niazi F, Green H, Calhoun BC, Sturgis C, et al. Breast tissue, oral and urinary microbiomes in breast cancer. Oncotarget 2017;8:88122–38.
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17. Komesu YM, Richter HE, Carper B, Dinwiddie DL, Lukacz ES, Siddiqui NY, et al. The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls. Int Urogynecol J 2018;29:1785–95.
18. Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, et al. Profiling the urinary microbiota in male patients with bladder cancer in China. Front Cell Infect Microbiol 2018;8:167.
19. Bresler L, Price TK, Hilt EE, Joyce C, Fitzgerald CM, Wolfe AJ. Female lower urinary tract microbiota do not associate with IC/PBS symptoms: a case-controlled study. Int Urogynecol J 2019;30:1835–42.
20. Kassiri B, Shrestha E, Kasprenski M, Antonescu C, Florea LD, Sfanos KS, et al. A Prospective study of the urinary and gastrointestinal microbiome in prepubertal males. Urology 2019;131:204–10.
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22. Liu F, Zhang N, Jiang P, Zhai Q, Li C, Yu D, et al. Characteristics of the urinary microbiome in kidney stone patients with hypertension. J Transl Med 2020;18:130.
23. Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, et al. Profiling the urinary microbiome in men with calcium-based kidney stones. BMC Microbiol 2020;20:41.
24. Ciabattini A, Olivieri R, Lazzeri E, Medaglini D. Role of the microbiota in the modulation of vaccine immune responses. Front Microbiol 2019;10:1305.

Article information Continued

Table 1.

Articles that studied the urinary microbiome in healthy individuals, or healthy controls in case-control studies

Study No. Sex Age Urine collection Microbiome
Siddiqui et al. [2] (2011) 8 F 27-67 yr CCU Lactobacillus, Prevotella, Gardnerella, Peptoniphilus, Dialister, Finegoldia, Anaerococcus, Allisonella, Streptococcus, Staphylococcus
Wolfe et al. [5] (2012) 12 F NA CCU, TUC, SPA Lactobacillus, Actinobaculum, Aerococcus, Anaerococcus, Atopobium, Burkholderia, Corynebacterium, Gardnerella, Prevotella, Ralstonia, Sneathia, Staphylococcus, Streptococcus, Veillonella
Fouts et al. [3] (2012) 11 M 24-50 yr MSU Corynebacterium, Staphylococcus, Streptococcus, Lactobacillus, Gardnerella, Veillonella
15 F 22-51 yr Lactobacillus, Corynebacterium, Staphylococcus, Streptococcus, Prevotella
Nelson et al. [4] (2012) 18 M 14-17 yr FCU Corynebacterium, Lactobacillus, Staphylococcus, Gardnerella, Streptococcus, Anaerococcus, Veillonella, Prevotella, Escherichia
Lewis et al. [6] (2013) 6 M 39-83 yr CCU Firmicutes
10 F 26-90 yr Firmicutes, Actinobacteria, Bacteroidetes
Hilt et al. [7] (2014) 24 F NA TUC Lactobacillus, Corynebacterium, Streptococcus, Actinomyces, Staphylococcus, Aerococcus, Gardnerella, Bifidobacterium, Actinobaculum
Pearce et al. [8] (2014) 58 F 35-65 yr TUC Lactobacillus, Gardnerella, Corynebacterium, Enterobacteriaceae, Anaerococcus, Bifidobacterium, Streptococcus, Staphylococcus, Sneathia, Peptoniphilus, Atopobium, Rhodanobacter, Trueperella, Alloscardovia, Veillonella
Karstens et al. [9] (2016) 10 F 58 (mean) TUC Anoxybacillus, Lactobacillus, Prevotella, Gardnerella, Arthrobacter, Escherichia, Shigella
Thomas-White et al. [10] (2016) 60 F 35-65 yr TUC Lactobacillus, Gardnerella, Staphylococcus, Streptococcus, Enterococcus, Bifidobacterium, Atopobium, Enterobacteriaceae
Wu et al. [15] (2017) 25 F 26 (mean) TUC Lactobacillaceae, Prevotellaceae, Enterobacteriaceae, Veillonellaceae, Tissierellaceae, Bifidobacteriales
Gottschick et al. [12] (2017) 49 F 19-62 yr MSU Lactobacillus crispatus
Abernethy et al. [11] (2017) 20 F 28-43 yr TUC Lactobacillus acidophilus
Wang et al. [14] (2017) 21 F 43 (mean) MSU Lactobacillus, Varibaculum, Porphyromonas, Prevotella, Bacteroides
Rani et al. [13] (2017) 5 F 27-63 yr MSU Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes
3 M
Wu et al. [18] (2018) 18 M 55.5 (mean) MSU Escherichia-Shigella, Staphylococcus, Streptococcus, Aeromonas, Acinetobacter, Bacteroides, Lactobacillus
Komesu et al. [17] (2018) 84 F 53 (mean) TUC Lactobacillus, Gardnerella, Tepidimonas, Prevotella
Bucevic Popovic et al. [16] (2018) 19 M 61-82 yr MSU Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria
Meriwether et al. [21] (2019) 18 F 33.7 (mean) MSU Lactobacillus, Prevotella
Bresler et al. [19] (2019) 20 F 48 (mean) MSU Lactobacillus
Kassiri et al. [20] (2019) 10 M 3 mo-8 yr TUC Staphylococcus, Varibaculum, Peptoniphilus, Actinobaculum
Xie et al. [23] (2020) 21 M 44.2 (mean) NA Acinetobacter, Prevotella, Oscillospira, Parabacteroides, Fusobacterium
Liu et al. [22] (2020) 9 M 58.9 (mean) TUC Gardnerella, Pontibacter, Sphingomonas, Prevotella, Propionibacterium
3 F

CCU, clean catch urine; TUC, transurethral catheter; SPA, suprapubic aspirate; MSU, midstream urine; FCU, first catch urine; NA, not available.