Skip to main content

Advertisement

SpringerLink
Log in

A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections — A Review

  • Lower Urinary Tract Symptoms and Voiding Dysfunction (J Sandhu, Section Editor)
  • Published:
Current Urology Reports Aims and scope Submit manuscript

Abstract

Purpose of Review

Greater availability of sequencing methods has broadened the knowledge of the urinary microbiome in an environment previously believed to be sterile. This review discusses internal and external influences that promote either a balance or a dysbiosis of the urinary tract and the future perspectives in understanding lower urinary tract infections.

Recent Findings

Efforts have been made to identify a “core” urinary microbiome in which Firmicutes and Bacteroidetes account for most of the bacterial representations. A shift to a Proteobacteria-dominant representation shapes the fingerprint of the infectious urinary microbiome; furthermore, the virome and the mycobiome are important modulators of the urinary microbiome, which have been recently explored to determine their role in the health-disease process of the lower urinary tract.

Summary

A disturbance of bacterial representation and diversity triggers a transition from health to disease; conversely, a functional cooperative interplay between the host and microbiome allows for basic metabolic and immune functions to take place.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

Papers of particular interest, published recently, have been highlighted as: •   Of importance •• Of major importance

  1. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nature Rev Genet. 2012.

  2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007.

  3. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010.

  4. Whiteside SA, Razvi H, Dave S, Reid G, Burton JP. The microbiome of the urinary tract - a role beyond infection. Nature Rev Urol. 2015.

  5. Aragón IM, Herrera-Imbroda B, Queipo-Ortuño MI, et al. The urinary tract microbiome in health and disease. Europ Urol Focus. 2018.

  6. Nelson DE, van der Pol B, Dong Q, et al. Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS ONE. 2010;5(11):1–7.

    Article  CAS  Google Scholar 

  7. Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol. 2011.

  8. Wolfe AJ, Toh E, Shibata N, et al. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 2012.

  9. Lewis DA, Brown R, Williams J, et al. The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol. 2013.

  10. Fouts DE, Pieper R, Szpakowski S, et al. Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in ground-breaking neuropathic bladder associated with spinal cord injury. J Transl Med [Internet]. 2012;10(1):1. Available from: Journal of Translational Medicine.

  11. Hilt EE, McKinley K, Pearce MM, et al. Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol. 2014.

  12. Pearce MM, Hilt EE, Rosenfeld AB, et al. The female urinary microbiome: A comparison of women with and without urgency urinary incontinence. MBio. 2014.

  13. Morand A, Cornu F, Dufour JC, Tsimaratos M, Lagier JC, Raoult D. Human bacterial repertoire of the urinary tract: a potential paradigm shift. J Clin Microbiol. 2018.

  14. Tang J. Microbiome in the urinary system—a review. AIMS Microbiol. 2017.

  15. Nelson A, De Soyza A, Perry JD, Sutcliffe IC, Cummings SP. Polymicrobial challenges to Koch’s postulates: ecological lessons from the bacterial vaginosis and cystic fibrosis microbiomes. Innate Immun. 2012;18(5):774–83.

    Article  CAS  Google Scholar 

  16. Hasman H, Saputra D, Sicheritz-Ponten T, et al. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. J Clin Microbiol. 2014.

  17. Moustafa A, Li W, Singh H, et al. Microbial metagenome of urinary tract infection. Sci Rep. 2018.

  18. Willner D, Low S, Steen JA, et al. Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. MBio. 2014.

  19. Santiago-Rodriguez TM, Ly M, Bonilla N, Pride DT. The human urine virome in association with urinary tract infections. Front Microbiol. 2015.

  20. Saralaya V, Shenoy S, Baliga S, Hegde A, Adhikari P, Chakraborty A. Characterization of Escherichia coli phylogenetic groups associated with extraintestinal infections in South Indian population. Ann Med Health Sci Res. 2015.

  21. Khasriya R, Sathiananthamoorthy S, Ismail S, et al. Spectrum of bacterial colonization associated with urothelial cells from patients with chronic lower urinary tract symptoms. J Clin Microbiol. 2013;51(7):2054–62.

    Article  Google Scholar 

  22. • Bajic P, Van Kuiken ME, Burge BK, et al. Male bladder microbiome relates to lower urinary tract symptoms. Eur Urol Focus [Internet]. 2020;6(2):376–82. Available from: https://doi.org/10.1016/j.euf.2018.08.001. This study evaluated the association between LUTS intensity and the ability of EQUC and sequencing methods to detect bacteria.

  23. Miller-Ensminger T, Garretto A, Brenner J, et al. Bacteriophages of the urinary microbiome. J Bacteriol. 2018.

  24. Garretto A, Miller-Ensminger T, Wolfe AJ, Putonti C. Bacteriophages of the lower urinary tract. Nat Rev Urol. 2019;16(7):422–32.

    Article  Google Scholar 

  25. Garretto A, Thomas-White K, Wolfe AJ, Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virol. 2018.

  26. Galtier M, De Sordi L, Maura D, et al. Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition. Environ Microbiol. 2016;18(7):2237–45.

    Article  CAS  Google Scholar 

  27. Ackerman AL, Underhill DM. The mycobiome of the human urinary tract: potential roles for fungi in urology. Ann Transl Med. 2017;5(2):1–12.

    Google Scholar 

  28. •• Nickel JC, Stephens A, Landis JR, et al. Urinary fungi associated with urinary symptom severity among women with interstitial cystitis/bladder pain syndrome (IC/BPS). World J Urol [Internet]. 2020;38(2):433–46. Available from: https://doi.org/10.1007/s00345-019-02764-0. This study used sequencing methods and mass spectrometry to assess how variations in the urinary mycobiome were associated with urinary tract symptoms.

  29. Paalanne N, Husso A, Salo J, et al. Intestinal microbiome as a risk factor for urinary tract infections in children. Eur J Clin Microbiol Infect Dis. 2018;37(10):1881–91.

    Article  Google Scholar 

  30. Jeney SES, Lane F, Oliver A, Whiteson K, Dutta S. Fecal microbiota transplantation for the treatment of refractory recurrent urinary tract infection. Obstet Gynecol. 2020;136(4):771–3.

    Article  Google Scholar 

  31. Magruder M, Sholi AN, Gong C, et al. Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection. Nat Commun [Internet]. 2019;10(1):1–9. Available from: https://doi.org/10.1038/s41467-019-13467-w.

  32. • Wolff BJ, Price TK, Joyce CJ, Wolfe AJ, Mueller ER. Oral probiotics and the female urinary microbiome: a double-blinded randomized placebo-controlled trial. Int Urol Nephrol [Internet]. 2019;51(12):2149–59. Available from: https://doi.org/10.1007/s11255-019-02282-3. Following oral probiotic randomization, this study found no change in the urine microbiota compared to controls.

  33. • Mulder M, Radjabzadeh D, Hassing RJ, et al. The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC Microbiol. 2019;19(1):1–7. This study evaluated the effects of antibiotics on the urinary microbiome. Changes in the microbiome may persist long after antibiotic use has stopped.

    Article  Google Scholar 

  34. Rani A, Ranjan R, McGee HS, et al. Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance. Transl Res. 2017.

  35. Den Heijer CDJ, Geerlings SE, Prins JM, Beerepoot MAJ, Stobberingh EE, Penders J. Can the composition of the intestinal microbiota predict the development of urinary tract infections? Future Microbiol. 2016;11(11):1395–404.

    Article  CAS  Google Scholar 

  36. Drake MJ, Morris N, Apostolidis A, Rahnama’i MS, Marchesi JR. The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015. Neurourology and Urodynamics. 2017.

  37. 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.

    Article  CAS  Google Scholar 

  38. Coorevits L, Heytens S, Boelens J, Claeys G. The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols. Eur J Clin Microbiol Infect Dis [Internet]. 2017;36(4):635–9. Available from. https://doi.org/10.1007/s10096-016-2839-x.

  39. Lee KW, Song HY, Kim YH. The microbiome in urological diseases. Investig Clin Urol. 2020;61(4):338–48.

    Article  Google Scholar 

  40. Horwitz D, McCue T, Mapes AC, et al. Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference. J Infect. 2015.

  41. Mueller ER, Wolfe AJ, Brubaker L, Opin C. The female urinary microbiota HHS public access author manuscript. Curr Opin Urol. 2017;27(3):282–6.

    Article  Google Scholar 

  42. Finucane TE. ‘Urinary tract infection’ and the microbiome. Am J Med [Internet]. 2017;130(3):e97–8. Available from. https://doi.org/10.1016/j.amjmed.2016.08.018.

  43. Miller-Ensminger T, Garretto A, Brenner J, et al. Bacteriophages of the urinary microbiome. J Bacteriol. 2018;200(7):1–13.

    Article  Google Scholar 

  44. Neugent ML, Hulyalkar NV, Nguyen VH, Zimmern PE, De Nisco NJ. Advances in understanding the human urinary microbiome and its potential role in urinary tract infection. MBio. 2020;11(2):1–15.

    Article  Google Scholar 

Download references

Acknowledgements

Dr. Sergio Lozano for text editing and revision.

Author information

Authors and Affiliations

  1. Department of Urology, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico

    Rigoberto Pallares-Mendez, Daniel E. Cervantes-Miranda, Alejandro Diaz Gonzalez-Colmenero, Mario A. Ochoa-Arvizo & Adrian Gutierrez-Gonzalez

Authors
  1. Rigoberto Pallares-Mendez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel E. Cervantes-Miranda
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alejandro Diaz Gonzalez-Colmenero
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mario A. Ochoa-Arvizo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Adrian Gutierrez-Gonzalez
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Protocol/Project development: Pallares-Mendez, Cervantes-Miranda, Guiterrez-Gonzalez. Data collection or management: Pallares-Mendez, Cervants-Miranda, Diaz Gonzalez-Colmenero, Gutierrez-Gonzalez, Ochoa-Arvizo. Manuscript writing editing: Pallares-Mendez, Cervantes-Miranda, Diaz Gonzalez-Colmenero, Ochoa-Arvizo, Gutierrez-Gonzalez.

Corresponding author

Correspondence to Rigoberto Pallares-Mendez.

Ethics declarations

Conflict of Interest

The authors have no conflict of interest to disclose.

Human and Animal Rights and Informed Consent

This article does not contain any studies with human or animal subjects perfomed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This article is part of the Topical Collection on Lower Urinary Tract Symptoms and Voiding Dysfunction

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pallares-Mendez, R., Cervantes-Miranda, D.E., Gonzalez-Colmenero, A.D. et al. A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections — A Review. Curr Urol Rep 23, 235–244 (2022). https://doi.org/10.1007/s11934-022-01108-7

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11934-022-01108-7

Keywords

Search

Navigation