Urinary microbiome and its relationship with urinary tract infections

Authors

Keywords:

microbioma urinario, infecciones del tracto urinario, disbiosis, probióticos, urobioma

Abstract

The urinary microbiome plays a central role in the pathophysiology of urinary tract infections, as its balance acts as a natural barrier against colonization by pathogens, and its alterations (dysbiosis) are associated with recurrent infections and increased susceptibility to infection. A qualitative systematic review was conducted of studies published between 2020 and 2025 in PubMed, Scopus, and Web of Science, which evaluated the composition of the urinary microbiome, its changes in the presence of infection, and its clinical implications. Twenty-eight articles met the inclusion criteria. The studies show that the urinary tract harbors complex microbial communities, with a predominance of genera such as Lactobacillus, Corynebacterium, and Streptococcus in healthy subjects, while in patients with recurrent infections, dysbiosis, loss of protective species, and an increase in opportunistic bacteria such as Escherichia coli, Enterococcus, and Klebsiella are observed, along with reduced microbial diversity. Furthermore, a gut-bladder axis is described whereby the gut microbiota can act as a reservoir for uropathogenic strains, promoting urinary colonization and the recurrence of infections. The integration of next-generation sequencing techniques and expanded cultures improves the characterization of the urinary microbiome and allows differentiation between dysbiosis and active infection. In conclusion, the evidence supports the urinary microbiome as a key component in urinary tract infections and suggests new diagnostic and therapeutic strategies aimed at restoring microbial balance, such as the use of probiotics and other ecological approaches, although controlled clinical trials are still needed to validate their efficacy and define their application in medical practice.

Downloads

Download data is not yet available.

References

Balaouras, G., Kostoulas, P., Mikos, T., Balaouras, D. & Chitzios, D. (2024). The Study of Microbiome of the Female Genital Area in Relation to Pelvic Floor Dysfunction: A Systematic Review. Springer Nature Link, 35, 1347–1362. https://doi.org/10.1007/s00192-024-05821-4

Bastidas-Caldes, C., Hernández-Alomía, F., Almeida, M., Ormaza, M., Boada, J., Graham, J., Calvopiña, M., & Castillejo, P. (2024). Molecular identification and antimicrobial resistance patterns of enterobacterales in community urinary tract infections among indigenous women in Ecuador: addressing microbiological misidentification. BMC infectious diseases, 24(1), 1195. https://doi.org/10.1186/s12879-024-10096-7

Bradley, E. S., Stansky, C., Zeamer, A. L., Huang, Z., Cincotta, L., Lopes, A., Potter, L., Fontes, T., Ward, D. V., Bucci, V., McCormick, B. A., & Haran, J. P. (2025). The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the emergency department. Virulence, 16(1), 2546063. https://doi.org/10.1080/21505594.2025.2546063

Corrales-Acosta, E., Cuartiella Zaragoza, E., Monzó Pérez, M., Benítez Perdomo, S., Corrales-Riveros, J. G., & Corrales, M. (2025). Prevention of Recurrent Urinary Tract Infection in Women: An Update. Microbiology Research, 16(3), 66. https://doi.org/10.3390/microbiolres16030066

Choi, J. H. et al (2024). Gut microbiome correlates of recurrent urinary tract infection. The Lancet eClinical Medicine, 66, 101900. https://doi.org/10.1016/j.eclinm.2024.102490

Choi, H. W., Lee, K. W. & Kim, Y. H. (2023). Microbiome in urological diseases: Axis crosstalk and bladder disorders. Investigative and Clinical Urology, 64(2), 126–139. https://doi.org/10.4111/icu.20220357

de Souza, H. D., Diório, G. R. M., Peres, S. V., Francisco, R. P. V., & Galletta, M. A. K. (2023). Bacterial profile and prevalence of urinary tract infections in pregnant women in Latin America: a systematic review and meta-analysis. BMC pregnancy and childbirth, 23(1), 774. https://doi.org/10.1186/s12884-023-06060-z

Flores-Oropeza, M. A., Ochoa, S. A., Cruz-Córdova, A., Chavez-Tepecano, R., Martínez-Peñafiel, E., Rembao-Bojórquez, D., Zavala-Vega, S., Hernández-Castro, R., Flores-Encarnacion, M., Arellano-Galindo, J., Vélez, D., & Xicohtencatl-

Cortes, J. (2024). Comparative genomic analysis of uropathogenic Escherichia coli strains from women with recurrent urinary tract infection. Frontiers in microbiology, 14, 1340427. https://doi.org/10.3389/fmicb.2023.1340427

Guo, H., Zhou, X., Li, Z., Zhi, J., Fu, C., Liu, X., Wu, Y., Liu, F., & Feng, N. (2025). Exploring the systemic impacts of urinary tract infection-specific antibiotic treatments on the gut microbiome, metabolome, and intestinal morphology in rats. PeerJ, 13, e19486. https://doi.org/10.7717/peerj.19486

He, Y., Zhao, J., Wang, L. et al. (2025). Epidemiological trends and predictions of urinary tract infections in the global burden of disease study 2021. Sci Rep, 15, 4702. https://doi.org/10.1038/s41598-025-89240-5

Jones-Freeman, B., Chonwerawong, M., Marcelino, V. R., Deshpande, A. V., Forster, S. C., & Starkey, M. R. (2021). The microbiome and host mucosal interactions in urinary tract diseases. Mucosal immunology, 14(4), 779–792. https://doi.org/10.1038/s41385-020-00372-5

Kim, D. S., & Lee, J. W. (2023). Urinary Tract Infection and Microbiome. Diagnostics, 13(11), 1921. https://doi.org/10.3390/diagnostics13111921

Magruder, M., Edusei, E., Zhang, L., Albakry, S., Satlin, M. J., Westblade, L. F., Crawford, C., … & Satlin, M. J. (2020). Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection. Gut

Microbes, 12(1), 1805281. https://doi.org/10.1080/19490976.2020.1805281

Mancuso, G., Midiri, A., Gerace, E., Marra, M., Zummo, S., & Biondo, C. (2023). Urinary Tract Infections: The Current Scenario and Future Prospects. Pathogens (Basel, Switzerland), 12(4), 623. https://doi.org/10.3390/pathogens12040623

Miller, S. J., Carpenter, L., Taylor, S. L., Wesselingh, S. L., Choo, J. M., Papanicolas, L. E., & Rogers, G. B. (2024). Intestinal microbiology and urinary tract infection associated risk in long-term aged care residents. Communications Medicine, 4, Article 164. https://doi.org/10.1038/s43856-024-00583-y

Naji, A., Roten, D. A., & Evans, R. T. (2024). Role of the gut, urine, and vaginal microbiomes in the pathogenesis and therapy of recurrent urinary tract infection. Open Forum Infectious Diseases, 11(9), ofae471. https://doi.org/10.1093/ofid/ofae471

Neugent, M. L., Hulyalkar, N. et al. (2020). Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. mBio, 11(2), e00218-20. https://doi.org/10.1128/mBio.00218-20

Pastuszka, A., Brantsæter, A., & Sokolowska, E. (2025). Rewriting the urinary tract paradigm: the urobiome as a novel biomarker for urinary tract health. Microbial Pathogenesis, 180, 106812. 10.1007/s11033-025-10609-w

Perez-Carrasco, V., Sanz-García, A., & Martínez-Martínez, L. (2021). Urinary Microbiome: Yin and Yang of the Urinary Tract. Frontiers in Cellular and Infection Microbiology, 11, 617002. https://doi.org/10.3389/fcimb.2021.617002

Reasoner, SA., Francis, J. & Hadjifrangiskou, M. (2025). The urinary microbiome: The next frontier of bacterial ecology. Journal of Bacteriology, 207(1), e00105-25. https://doi.org/10.1128/jb.00105-25

Saenz, C. N., Ko, E. Y., & Davies, K. P. (2025). The human urinary microbiome and its potential role in urinary tract infection. Seminars in Nephrology, 45(2), 157-167. https://doi.org/10.1016/j.euf.2024.12.005

Salazar, A. M., Neugent, M. L., De Nisco, N. J., & Mysorekar, I. U. (2022). Gut-bladder axis enters the stage: Implication for recurrent urinary tract infections. Cell host & microbe, 30(8), 1066–1069. https://doi.org/10.1016/j.chom.2022.07.008

Seo, H. Kim, S. (2025). Emerging insights into microbiome therapeutics for urinary tract infection. EUTI, 20(1), 4–16. https://doi.org/10.14777/uti.2448034017

Ravel J., Simmons, Sh., Greenwood, E., Gottfried, S. et al. (2025). Impact of a multi-strain L. crispatus-based vaginal synbiotic on the vaginal microbiome: a randomized placebo-controlled trial. Biofilms and microbiomes, 11, 158. https://doi.org/10.1038/s41522-025-00788-6

Weng, X., Liu, Y., Hu, H., Wang, M., & Huang, X. (2023). Changes of microbiota level in urinary tract infections: A meta-analysis. Open medicine (Warsaw, Poland), 18(1), 20230702. https://doi.org/10.1515/med-2023-0702

Worby, C. J., Olson, B. S., Dodson, K. W., Earl, A. M., & Hultgren, S. J. (2022). Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections. Journal of Clinical Investigation, 132(5), e158497. https://doi.org/10.1172/JCI158497

Yang, X., Chen, H., Zheng, Y., Qu, S., Wang, H., & Yi, F. (2022). Disease burden and long-term trends of urinary tract infections: A worldwide report. Frontiers in public health, 10, 888205. https://doi.org/10.3389/fpubh.2022.888205

Zhang, J., et al. (2025). Exploring urinary microbiome: Insights into neurogenic bladder and improving management of urinary tract infections. Frontiers in Cellular and Infection Microbiology, 15, 1512891. https://doi.org/10.3389/fcimb.2025.1512891

Published

2026-01-15

How to Cite

Urinary microbiome and its relationship with urinary tract infections. (2026). Opuntia Brava, 18(1), 74-87. https://opuntiabrava.ult.edu.cu/index.php/opuntiabrava/article/view/2856