The urine microbiome: what's normal and what's pathological? Microbiome-based treatment and prevention of urinary tract infections: A review
- Authors: Zakharova I.N.1, Osmanov I.M.2,3, Bekmurzaeva G.B.1,2, Anisimova P.D.1, Churilova V.D.1
-
Affiliations:
- Russian Medical Academy of Continuous Professional Education
- Bashlyaeva Children's City Clinical Hospital
- Pirogov Russian National Research Medical University (Pirogov University)
- Issue: No 4 (2025)
- Pages: 327-336
- Section: Articles
- URL: https://ogarev-online.ru/2658-6630/article/view/381445
- DOI: https://doi.org/10.26442/26586630.2025.4.203547
- ID: 381445
Cite item
Full Text
Abstract
Research on the urine microbiome dates back approximately 150 years. Historically, the prevailing view was that the urinary system of a healthy individual is sterile. This paradigm, which seemed unshakable, defined approaches to diagnosing and treating urinary tract infections. Only in the last few decades has the scientific community's opinion on this issue changed radically. Progress in microbiological research has enabled the use of advanced culture and novel molecular genetic methods to identify microorganisms inhabiting the urinary tract. Finally, the well-established dogma of the urine sterility in a healthy person was shattered. Not only bacteria but also viruses and fungi are found in the urine. There is currently no consensus on which composition of the urine microbiota should be considered normal. However, the accumulated data indicate that changes in the urobiome's taxonomic composition can serve as predictors of various pathological processes. The underlying pathogenetic mechanisms remain to be further studied. A correlation has been identified between altered urinary microbiota and the development of both inflammatory and non-inflammatory diseases, in particular, benign prostatic hyperplasia, interstitial cystitis/painful bladder syndrome, urolithiasis, overactive bladder, urinary incontinence, and even bladder cancer. Of particular relevance in pediatric practice is the search for methods to prevent and treat urinary tract infections, thereby preserving and maintaining the diversity of microorganisms colonizing this system. One such method is the use of combined herbal medicinal products, such as Canephron N, which has diverse effects due to its active components. A distinctive feature of this herbal medicinal product, along with its multifaceted therapeutic effect, is its antimicrobial activity without inhibiting the commensal microbiota of the urinary tract. Canephron N is a valuable tool in the pediatrician's arsenal, helping maintain the fragile balance of the urobiome and prevent several pathological conditions.
About the authors
Irina N. Zakharova
Russian Medical Academy of Continuous Professional Education
Author for correspondence.
Email: zakharova-rmapo@yandex.ru
ORCID iD: 0000-0003-4200-4598
D. Sci. (Med.), Prof.
Russian Federation, MoscowIsmail M. Osmanov
Bashlyaeva Children's City Clinical Hospital; Pirogov Russian National Research Medical University (Pirogov University)
Email: zakharova-rmapo@yandex.ru
ORCID iD: 0000-0003-3181-9601
D. Sci. (Med.), Prof.
Russian Federation, Moscow; MoscowGulfizat B. Bekmurzaeva
Russian Medical Academy of Continuous Professional Education; Bashlyaeva Children's City Clinical Hospital
Email: zakharova-rmapo@yandex.ru
Cand. Sci. (Med.)
Russian Federation, Moscow; MoscowPolina D. Anisimova
Russian Medical Academy of Continuous Professional Education
Email: zakharova-rmapo@yandex.ru
ORCID iD: 0009-0007-4550-1502
Graduate Student
Russian Federation, MoscowViktoriya D. Churilova
Russian Medical Academy of Continuous Professional Education
Email: zakharova-rmapo@yandex.ru
ORCID iD: 0009-0009-0335-0704
Assistant
Russian Federation, MoscowReferences
- Prescott SL. History of medicine: Origin of the term microbiome and why it matters. Human Microbiome Journal. 2017;4:24-5. doi: 10.1016/j.humic.2017.05.004
- Sender R, Fuchs S, Milo R. Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. 2016;164(3):337-40. doi: 10.1016/j.cell.2016.01.013
- Reasoner SA, Francis J, Hadjifrangiskou M. The urinary microbiome: the next frontier of bacterial ecology. J Bacteriol. 2025;207(8):e0010525. doi: 10.1128/jb.00105-25
- Kass EH. Asymptomatic infections of the urinary tract. Trans Assoc Am Physicians. 1956;69:56-64.
- Maskell RM. The natural history of urinary tract infection in women. Med Hypotheses. 2010;74(5):802-6. doi: 10.1016/j.mehy.2009.12.011
- Perez-Carrasco V, Soriano-Lerma A, Soriano M, et al. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front Cell Infect Microbiol. 2021;11:617002. doi: 10.3389/fcimb.2021.617002
- Price TK, Dune T, Hilt EE, et al. The Clinical Urine Culture: Enhanced Techniques Improve Detection of Clinically Relevant Microorganisms. J Clin Microbiol. 2016;54(5):1216-22. doi: 10.1128/JCM.00044-16
- Слесаревская М.Н., Кузьмин И.В., Жумадиллаев К.Г., и др. Микробиом и микробиота мочи: современные представления и гендерные особенности. Урологические ведомости. 2022;12(2):157-65 [Slesarevskaya MN, Kuzmin IV, Zhumadillayev KG, et al. Microbiome and urine microbiota: modern concepts and gender features. Urology reports (St.-Petersburg). 2022;12(2):157-65 (in Russian)]. doi: 10.17816/uroved109278
- Pearce MM, Hilt EE, Rosenfeld AB, et al. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. mBio. 2014;5(4):e01283-14. doi: 10.1128/mBio.01283-14
- Carrigg C, Rice O, Kavanagh S, et al. DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol. 2007;77(4): 955-64. doi: 10.1007/s00253-007-1219-y
- Felczykowska A, Krajewska A, Zielińska S, Łoś JM. Sampling, metadata and DNA extraction – important steps in metagenomic studies. Acta Biochim Pol. 2015;62(1):151-60. doi: 10.18388/abp.2014_916
- Bukin YS, Galachyants YP, Morozov IV, et al. The effect of 16S rRNA region choice on bacterial community metabarcoding results. Sci Data. 2019;6:190007. doi: 10.1038/sdata.2019.7
- Kim JK, Song SH, Jung G, et al. Possibilities and limitations of using low biomass samples for urologic disease and microbiome research. Prostate Int. 2022;10(4):169-80. doi: 10.1016/j.prnil.2022.10.001
- LaRocco MT, Franek J, Leibach EK, et al. Effectiveness of Preanalytic Practices on Contamination and Diagnostic Accuracy of Urine Cultures: a Laboratory Medicine Best Practices Systematic Review and Meta-analysis. Clin Microbiol Rev. 2016;29(1):105-47. doi: 10.1128/CMR.00030-15
- Pohl HG, Groah SL, Pérez-Losada M, et al. The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method. Int Neurourol J. 2020;24(1):41-51. doi: 10.5213/inj.1938244.122
- Du J, Khemmani M, Halverson T, et al. Cataloging the phylogenetic diversity of human bladder bacterial isolates. Genome Biol. 2024;25(1):75. doi: 10.1186/s13059-024-03216-8
- Kinneman L, Zhu W, Wong WSW, et al. Assessment of the Urinary Microbiome in Children Younger Than 48 Months. Pediatr Infect Dis J. 2020;39(7):565-70. doi: 10.1097/INF.0000000000002622
- Storm DW, Copp HL, Halverson TM, et al. A Child’s urine is not sterile: A pilot study evaluating the Pediatric Urinary Microbiome. J Pediatr Urol. 2022;18(3):383-92. doi: 10.1016/j.jpurol.2022.02.025
- Qin J, Shi X, Xu J, et al. Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals. Front Microbiol. 2021;12:673969. doi: 10.3389/fmicb.2021.673969
- Roth RS, Liden M, Huttner A. The urobiome in men and women: a clinical review. Clin Microbiol Infect. 2023;29(10):1242-48. doi: 10.1016/j.cmi.2022.08.010
- Pearce MM, Zilliox MJ, Rosenfeld AB, et al. The female urinary microbiome in urgency urinary incontinence. Am J Obstet Gynecol. 2015;213(3):347.e1-11. doi: 10.1016/j.ajog.2015.07.009
- Siddiqui NY, Ma L, Brubaker L, et al. Updating Urinary Microbiome Analyses to Enhance Biologic Interpretation. Front Cell Infect Microbiol. 2022;12:789439. doi: 10.3389/fcimb.2022.789439
- Ammitzbøll N, Bau BPJ, Bundgaard-Nielsen C, et al. Pre- and postmenopausal women have different core urinary microbiota. Sci Rep. 2021;11(1):2212. doi: 10.1038/s41598-021-81790-8
- Nickel JC, Stephens A, Ackerman AL, et al. The healthy urinary microbiome in asymptomatic participants in the MAPP Network Study: Relation to gender, age, and menopausal status. Can Urol Assoc J. 2022;16(9):E448-54. doi: 10.5489/cuaj.7775
- Bowie KR, Garzotto M, Orwoll E, Karstens L. Body mass index and benign prostatic hyperplasia correlate with urinary microbiome diversity and lower urinary tract symptoms in men. Commun Med (Lond). 2025;5(1):159. doi: 10.1038/s43856-025-00866-y
- Price TK, Lin H, Gao X, et al. Bladder bacterial diversity differs in continent and incontinent women: a cross-sectional study. Am J Obstet Gynecol. 2020;223(5):729.e1-729.e10. doi: 10.1016/j.ajog.2020.04.033
- Zárate S, Taboada B, Yocupicio-Monroy M, Arias CF. Human Virome. Arch Med Res. 2017;48(8):701-16. doi: 10.1016/j.arcmed.2018.01.005
- Santiago-Rodriguez TM, Ly M, Bonilla N, Pride DT. The human urine virome in association with urinary tract infections. Front Microbiol. 2015;6:14. doi: 10.3389/fmicb.2015.00014
- Atkinson AL, Atwood WJ. Fifty Years of JC Polyomavirus: A Brief Overview and Remaining Questions. Viruses. 2020;12(9):969. doi: 10.3390/v12090969
- Garretto A, Miller-Ensminger T, Wolfe AJ, Putonti C. Bacteriophages of the lower urinary tract. Nat Rev Urol. 2019;16(7):422-32. doi: 10.1038/s41585-019-0192-4
- Hassall A. On the Development of Torulæ in the Urine, and on the relation of these Fungi to Albuminous and Saccharine Urine. Med Chir Trans. 1853;36:23-78.9. doi: 10.1177/095952875303600103
- Ghannoum MA, Jurevic RJ, Mukherjee PK, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010;6(1):e1000713. doi: 10.1371/journal.ppat.1000713
- Ackerman AL, Underhill DM. The mycobiome of the human urinary tract: potential roles for fungi in urology. Ann Transl Med. 2017;5(2):31. doi: 10.21037/atm.2016.12.69
- Flores-Mireles AL, Walker JN, Caparon M, Hultgren SJ. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol. 2015;13(5):269-84. doi: 10.1038/nrmicro3432
- Robino L, Navarro N, Canales-Huerta N, et al. Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections. Microbiol Spectr. 2025;13(11). doi: 10.1128/spectrum.01247-25
- Whiteside SA, Razvi H, Dave S, et al. The microbiome of the urinary tract – a role beyond infection. Nat Rev Urol. 2015;12(2):81-90. doi: 10.1038/nrurol.2014.361
- Karlsson M, Scherbak N, Reid G, Jass J. Lactobacillus rhamnosus GR-1 enhances NF-kappaB activation in Escherichia coli-stimulated urinary bladder cells through TLR4. BMC Microbiol. 2012;12:15. doi: 10.1186/1471-2180-12-15
- Ohlemacher SI, Giblin DE, d’Avignon DA, et al. Enterobacteria secrete an inhibitor of Pseudomonas virulence during clinical bacteriuria. J Clin Invest. 2017;127(11): 4018-30. doi: 10.1172/JCI92464
- Lai HC, Chang SN, Lin HC, et al. Association between urine pH and common uropathogens in children with urinary tract infections. J Microbiol Immunol Infect. 2021;54(2):290-8. doi: 10.1016/j.jmii.2019.08.002
- Shrestha LB, Baral R, Poudel P, Khanal B. Clinical, etiological and antimicrobial susceptibility profile of pediatric urinary tract infections in a tertiary care hospital of Nepal. BMC Pediatr. 2019;19(1):36. doi: 10.1186/s12887-019-1410-1
- Höller M, Steindl H, Abramov-Sommariva D, et al. Treatment of Urinary Tract Infections with Canephron(®) in Germany: A Retrospective Database Analysis. Antibiotics (Basel). 2021;10(6):685. doi: 10.3390/antibiotics10060685
- Brenneis C, Künstle G, Haunschild J. Spasmolytic activity of Canephron N on the contractility of rat and human isolated urinary bladder. In: Proceedings of the 13th Congress of the International Society for Ethnopharmacology. Graz, Austria, 2012.
- Sihra N, Goodman A, Zakri R, et al. Nonantibiotic prevention and management of recurrent urinary tract infection. Nat Rev Urol. 2018;15(12):750-76. doi: 10.1038/s41585-018-0106-x
- Wagenlehner FM, Abramov-Sommariva D, Höller M, et al. Non-Antibiotic Herbal Therapy (BNO 1045) versus Antibiotic Therapy (Fosfomycin Trometamol) for the Treatment of Acute Lower Uncomplicated Urinary Tract Infections in Women: A Double-Blind, Parallel-Group, Randomized, Multicentre, Non-Inferiority Phase III Trial. Urol Int. 2018;101(3):327-36. doi: 10.1159/000493368
- Давидов М.И., Бунова Н.Е. Сравнительная оценка монотерапии препаратами Канефрон Н и ципрофлоксацин острого неосложненного цистита у женщин. Урология. 2018;(4):24-32 [Davidov MI, Bunova NE. Comparative assessment of Canephron N and ciprofloxacin as monotherapy of acute uncomplicated cystitis in women. Urologiia. 2018;(4):24-32 (in Russian)].
- Вознесенская Т.С., Кутафина Е.К. Фитотерапия в лечении инфекции мочевой системы у детей. Педиатрическая фармакология. 2007;4(5):38-40 [Voznesenskaia TS, Kutafina EK. Fitoterapiia v lechenii infektsii mochevoi sistemy u detei. Pediatricheskaia farmakologiia. 2007;4(5):38-40 (in Russian)].
- Сукало А.В., Крохина С.А., Тур Н.И. Применение препарата Канефрон в комплексной терапии инфекций мочевой системы у детей. Медицинские новости. 2004;11:84-6 [Sukalo AV, Krokhina SA, Tur NI. Preparation Canephron® N use in complex therapy of urinary system infections in children. Medical News. 2004;11:84-6 (in Russian)].
- Инфекция мочевых путей у детей. Клинические рекомендации. 2024. Режим доступа: https://cr.minzdrav.gov.ru/view-cr/281_3. Ссылка активна на 08.10.2025 [Infektsiia mochevykh putei u detei. Klinicheskie rekomendatsii. 2024. Available at: https://cr.minzdrav.gov.ru/view-cr/281_3. Accessed: 08.10.2025 (in Russian)].
- Abbasian B, Shair A, O’Gorman DB, et al. Potential Role of Extracellular ATP Released by Bacteria in Bladder Infection and Contractility. mSphere. 2019;4(5):e00439-19. doi: 10.1128/mSphere.00439-19
- Komesu YM, Richter HE, Carper B, et al. The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls. Int Urogynecol . 2018;29(12):1785-95. doi: 10.1007/s00192-018-3683-6
- Carnes MU, Siddiqui NY, Karstens L, et al. Urinary microbiome community types associated with urinary incontinence severity in women. Am J Obstet Gynecol. 2024;230(3):344.e1-344.e20. doi: 10.1016/j.ajog.2023.10.036
- Pearle MS, Goldfarb DS, Assimos DG, et al. Medical management of kidney stones: AUA guideline. J Urol. 2014;192(2):316-24. doi: 10.1016/j.juro.2014.05.006
- Zampini A, Nguyen AH, Rose E, et al. Defining Dysbiosis in Patients with Urolithiasis. Sci Rep. 2019;9(1):5425. doi: 10.1038/s41598-019-41977-6
- Kachroo N, Monga M, Miller AW. Comparative functional analysis of the urinary tract microbiome for individuals with or without calcium oxalate calculi. Urolithiasis. 2022;50(3):303-17. doi: 10.1007/s00240-022-01314-5
- Noonin C, Putpim A, Thongboonkerd V. The direct inhibitory effects of Lactobacillus acidophilus, a commensal urinary bacterium, on calcium oxalate stone development. Microbiome. 2024;12(1):175. doi: 10.1186/s40168-024-01877-y
- Liu F, Zhang N, Wu Y, et al. The pelvis urinary microbiome in patients with kidney stones and clinical associations. BMC Microbiol. 2020;20(1):336. doi: 10.1186/s12866-020-01992-4
- Barr-Beare E, Saxena V, Hilt EE, et al. The Interaction between Enterobacteriaceae and Calcium Oxalate Deposits. PLoS One. 2015;10(10):e0139575. doi: 10.1371/journal.pone.0139575
- Bichler K, Eipper E, Naber K, et al. Urinary infection stones. Int J Antimicrob Agents. 2002;19(6):488-98. doi: 10.1016/s0924-8579(02)00088-2
- Shen C, Zhu Q, Dong F, et al. Identifying Two Novel Clusters in Calcium Oxalate Stones With Urinary Tract Infection Using 16S rDNA Sequencing. Front Cell Infect Microbiol. 2021;11:723781. doi: 10.3389/fcimb.2021.723781
- EAU Guidelines. Edn. presented at the EAU Annual Congress Madrid 2025. EAU Guidelines Office, Arnhem, the Netherlands. Available at: http://uroweb.org/guidelines/compilations-of-all-guidelines. Accessed: 08.10.2025.
- Coco C, Jacobs M. Surgical indications for operative management of vesicoureteral reflux in children. Current Opinion in Pediatrics. 2021;33(2):243-4. doi: 10.1097/mop.0000000000001000
Supplementary files

