A modern view of the urinary tract microbiome
Keywords:
urinary tract microbiome, healthy microbiome, chronic urinary tract infections, microbiome correction, intestinal microflora, synbiotics
Abstract
This review presents the latest date on the urinary tract microbiome (UTM). Finding of a resident microbiome of UTM has become an unexpected discovery in recent years. It was found that slow-growing fastidious or nutritionally demanding species, including anaerobic bacteria, predominate among the microbial inhabitants of the UTM. In this regard, there is an urgent need to revise some aspects of generally accepted diagnostic schemes, the picture of pathogenesis and approaches to the treatment of urinary tract infections, which previously based on the idea of the urinary tract sterility. The concept of a “healthy microbiome” of the urinary tract continues to be developed. The need to compare microbiological findings with the clinical signs was once again confirmed. It has been shown that changes in the intestinal microbial community directly affect the microflora of urinary tract. Therefore, one of the promising approaches for the treatment of chronic urinary tract infections is considered to be the creation of complex multicomponent synbiotics including normal inhabitants of the intestinal tract and substrates necessary for their growth. Probiotics, fecal transplantation and special diets are already used in the complex treatment of chronic urinary tract infections. The avalanche-like growth in the number of the human microbiome studies allows us to expect significant progress in their practical application in the near future.
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References
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2. Lloyd-Price J., Mahurkar A., Rahnavard G., Crabtree J., Orvis J., Hall A.B., et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017;550(7674):61–66. https://doi.org/10.1038/nature23889
3. Aragón I.M., Herrera-Imbroda B., Queipo-Ortuño M.I., Castillo E., Del Moral J.S.-G., Gómez-Millán J., et al. The urinary tract microbiome in health and disease. Eur. Urol. Focus. 2018;4(1):128–138. https://doi.org/10.1016/j.euf.2016.11.001
4. Magistro G., Stief C.G. The urinary tract microbiome: the answer to all our open questions? Eur. Urol. Focus. 2019;5(1):36–38. https://doi.org/10.1016/j.euf.2018.06.011
5. Gilbert J.A., Blaser M.J., Caporaso J.G., Jansson J.K., Lynch S.V., Knight R. Current understanding of the human microbiome. Nat. Med. 2018;24(4):392–400. https://doi.org/10.1038/nm.4517
6. Shannon M.B., Limeira R., Johansen D., Gao X., Lin H., Dong Q., et al. Bladder urinary oxygen tension is correlated with urinary microbiota composition. Int. Urogynecol. J. 2019;30(8):1261–1267. https://doi.org/10.1007/s00192-019-03931-y
7. Amabebe E., Anumba D. The vaginal microenvironment: the physiologic role of lactobacilli. Front. Med. (Lausanne). 2018;5:181. https://doi.org/10.3389/fmed.2018.00181 eCollection 2018.
8. Reitzer L., Zimmern P. Rapid growth and metabolism of uropathogenic Escherichia coli in relation to urine composition. Clin. Microbiol. Rev. 2019;33(1):e00101-e00119. https://doi.org/10.1128/CMR.00101-19
9. Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. 2018. Improving saliva shotgun metagenomics by chemical host DNA depletion. Microbiome 6:42. doi: 10.1186/s40168-018-0426-3.
10. Brubaker L., Wolfe A.J. The female urinary microbiota, urinary health and common urinary disorders. Ann. Transl. Med. 2017;5(2):34. https://doi.org/10.21037/atm.2016.11.62
11. Hilt E.E., McKinley K., Pearce M.M., Rosenfeld A.B., Zilliox M.J., Mueller E.R., 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;52(3):871–876. https://doi.org/10.1128/JCM.02876-13
12. Price T.K., Dune T., Hilt E.E., Thomas-White K.J., Kliethermes S., Brincat C., et al. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J. Clin. Microbiol. 2016;54(5):1216–1222. https://doi .org/10.1128/JCM.00044-16
13. Thomas-White K., Forster S.C., Kumar N., Van Kuiken M., Putonti C., Stares M.D., et al. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nat. Commun. 2018;9(1):1557. https://doi.org/10.1038/s41467-018-03968-5
14. Price T.K., Hilt E.E., Thomas-White K., Mueller E.R., Wolfe A.J., Brubaker L. The urobiome of continent adult women: a cross-sectional study. BJOG. 2020;127(2):193–201. https://doi.org/10.1111/1471-0528.15920
15. Moustafa A., Li W., Singh H., Moncera K.J., Torralba M.G., Yu Y., et al. Microbial metagenome of urinary tract infection. Sci. Rep. 2018;8(1):4333. https://doi.org/10.1038/s41598-018-22660-8
16. Quince C., Walker A.W., Simpson J.T., Loman N.J., Segata N. Shotgun metagenomics, from sampling to analysis. Nat. Biotechnol. 2017;35(9):833–844. https://doi.org/10.1038/nbt.3935
17. Karstens L., Asquith M., Caruso V., Rosenbaum J.T., Fair D.A., Braun J., et al. Community profiling of the urinary microbiota: considerations for low-biomass samples. Nat. Rev. Urol. 2018;15(12):735–749. https://doi.org/10.1038/s41585-018-0104-z
18. Barraud O., Ravry C., Francois B., Daix T., Ploy M.C., Vignon P. Shotgun metagenomics for microbiome and resistome detection in septic patients with urinary tract infections. Int. J. Antimicrob. Agents. 2019;54(6):803–808. https://doi.org/10.1016/j.ijantimicag.2019.09.009
19. Medina M., Castillo-Pino E. An introduction to the epidemiology and burden of urinary tract infections. Ther. Adv. Urol. 2019 May 2;11:1756287219832172. https://doi.org/10.1177/1756287219832172
20. Whelan S., Lucey B., Finn K. Uropathogenic Escherichia coli (UPEC)-Associated Urinary Tract Infections: The Molecular Basis for Challenges to Effective Treatment. Microorganisms. 2023 Aug 28;11(9):2169. https://doi.org/10.3390/microorganisms11092169
21. Zilberberg M.D., Nathanson B.H., Sulham K., Shorr A.F. Descriptive epidemiology and outcomes of emergency department visits with complicated urinary tract infections in the United States, 2016-2018. J. Am. Coll. Emerg. Physicians Open. 2022 Mar 17;3(2):e12694. https://doi.org/10.1002/emp2.12694
22. Öztürk R., Murt A. Epidemiology of urological infections: a global burden. World J. Urol. 2020 Nov;38(11):2669-2679. https://doi.org/10.1007/s00345-019-03071-4
23. Baars C., van Ginkel C., Heesakkers J., Scholtes M., Martens F., Janssen D. The Burden of Urinary Tract Infections on Quality of Life and Healthcare in Patients with Interstitial Cystitis. Healthcare (Basel). 2023 Oct 18;11(20):2761. https://doi.org/10.3390/healthcare11202761
24. De Nisco N.J., Neugent M., Mull J., Chen L., Kuprasertkul A., de Souza Santos M., et al. Direct detection of tissue-resident bacteria and chronic inflammation in the bladder wall of postmenopausal women with recurrent urinary tract infection. J. Mol. Biol. 2019 Oct 4;431(21):4368–4379. https://doi.org/10.1016/j.jmb.2019.04.008
25. Forde B.M., Roberts L.W., Phan M.D., Peters K.M., Fleming B.A., Russell C.W., et al. Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection. Nat. Commun. 2019 Aug 13;10(1):3643. https://doi.org/10.1038/s41467-019-11571-5
26. Bolte L.A., Vich Vila A., Imhann F., Collij V., Gacesa R., Peters V., et al. Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Gut. 2021 Jul;70(7):1287-1298. https://doi.org/10.1136/gutjnl-2020-322670
27. Chiba M., Tsuji T., Komatsu M. Therapeutic advancement in inflammatory bowel disease by incorporating plant-based diet. Transl. Gastroenterol. Hepatol. 2023 Sep 12;8:38. https://doi.org/10.21037/tgh-23-6 eCollection 2023.
28. Matzaras R., Anagnostou N., Nikopoulou A., Tsiakas I., Christaki E. The Role of Probiotics in Inflammation Associated with Major Surgery: A Narrative Review. Nutrients. 2023 Mar 8;15(6):1331. https://doi.org/10.3390/nu15061331
29. Kim Y.B., Whon T.W., Kim J.Y., Kim J., Kim Y., Lee S.H., et al. In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract. Sci Rep. 2023 Jul 20;13(1):11746. https://doi.org/10.1038/s41598-023-38710-9
30. Mulder M., Radjabzadeh D., Hassing R.J., Heeringa J., Uitterlinden A.G., Kraaij R., et al. The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC Microbiol. 2019 Jan 9;19(1):9. https://doi.org/10.1186/s12866-018-1379-1
Published
2024-04-11
How to Cite
Evdokimova N. V., Chernenkaya T. V. A modern view of the urinary tract microbiome // Patologicheskaya Fiziologiya i Eksperimental’naya Terapiya (Pathological physiology and experimental therapy). 2024. VOL. 68. № 1. PP. 138–144.
Issue
Section
Reviews
