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Dysbiosis of the Human Urinary Microbiome and its Association to Diseases Affecting the Urinary System

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Abstract

The human urinary microbiome, also termed urobiome, has been overlooked due to the clinical dogma of sterile urine, as reported by routine culture. However, evolving sensitive tools such as expanded quantitative urine culture, 16S ribosomal RNA gene sequencing, and next-generation sequencing have discovered a vast number of microorganisms present in urine, even in healthy individuals. Microbiome dysbiosis and its links to disease is a heavily explored area in several microbial niches. Presently, urobiome dysbiosis and its correlation to urinary system-related diseases is at its infancy but rapidly emerging, as it provides potential therapeutic insights. This review outlines the changes in the human urinary microbiome concerning globally prevalent diseases affecting kidney function, such as chronic kidney disease (CKD), diabetes mellitus (DM), hypertension (HT), and urinary tract infection (UTI). Alterations to urine microbial diversity, including differences in the abundance and species richness of particular microbial genera, notably Lactobacillus, Prevotella, Streptococcus, Staphylococcus, Klebsiella, Enterococcus, between diseased and healthy samples are discussed utilising studies to date. Subsequent research needs to move beyond correlation to understand the roles of the urinary microbiota in diseases, thereby clarifying whether urinary dysbiosis has causal contributions that may provide important insight for diagnostics, pathophysiology, and therapy in renal pathologies.

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References

  1. Sender R, Fuchs S, Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14:e1002533. https://doi.org/10.1371/journal.pbio.1002533

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Ogunrinola GA, Oyewale JO, Oshamika OO, Olasehinde GI (2020) The human microbiome and its impacts on health. Int J Microbiol 2020:8045646. https://doi.org/10.1155/2020/8045646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bäckhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, Versalovic J, Young V, Finlay BB (2012) Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe 12:611–622. https://doi.org/10.1016/j.chom.2012.10.012

    Article  CAS  PubMed  Google Scholar 

  4. Mohajeri MH, Brummer RJ, Rastall RA, Weersma RK, Harmsen HJ, Faas M, Eggersdorfer M (2018) The role of the microbiome for human health: from basic science to clinical applications. Eur J Nutr 57:1–4. https://doi.org/10.1007/s00394-018-1703-4

    Article  PubMed  PubMed Central  Google Scholar 

  5. Dimitri-Pinheiro S, Soares R, Barata P (2020) The microbiome of the nose—friend or foe? Allergy Rhinol 11:2152656720911605. https://doi.org/10.1177/2152656720911605

    Article  Google Scholar 

  6. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804–810. https://doi.org/10.1038/nature06244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG (2010) The human oral microbiome. J Bacteriol 192:5002–5017. https://doi.org/10.1128/JB.00542-10

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Shreiner AB, Kao JY, Young VB (2015) The gut microbiome in health and in disease. Curr Opin Gastroenterolo 31:69–75. https://doi.org/10.1097/mog.0000000000000139

    Article  CAS  Google Scholar 

  9. Grice EA, Segre JA (2011) The skin microbiome. Nat Rev Microbiol 9:244–253. https://doi.org/10.1038/nrmicro253

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Mahdavinia M, Keshavarzian A, Tobin MC, Landay AL, Schleimer RP (2016) A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS). Clin Exp Allergy 46:21–41. https://doi.org/10.1111/cea.12666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ma B, Forney LJ, Ravel J (2012) Vaginal microbiome: rethinking health and disease. Ann Rev Microbiol 66:371–389. https://doi.org/10.1146/annurev-micro-092611-150157#

    Article  CAS  Google Scholar 

  12. Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoblach S, Suh MJ, Huang ST, Ljungberg I, Sprague BM, Lucas SK, Torralba M (2012) Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury. J Transl Med 10:1–7. https://doi.org/10.1186/1479-5876-10-174

    Article  CAS  Google Scholar 

  13. Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ, Mueller ER, Brubaker L, Gai X, Wolfe AJ, Schreckenberger PC (2014) Urine is not sterile: use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder. J Clin Microbiol 52:871–876. https://doi.org/10.1128/jcm.02876-13

    Article  PubMed  PubMed Central  Google Scholar 

  14. Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S, Brincat C, Brubaker L, Wolfe AJ, Mueller ER, Schreckenberger PC (2016) The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol 54:1216–1222. https://doi.org/10.1128/jcm.00044-16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD (2010) Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS ONE 5:e14116. https://doi.org/10.1371/journal.pone.0014116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS (2011) Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiol 11:244. https://doi.org/10.1186/1471-2180-11-244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Wolfe AJ, Toh E, Shibata N, Rong R, Kenton K, FitzGerald M, Mueller ER, Schreckenberger P, Dong Q, Nelson DE, Brubaker L (2012) Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol 50:1376–1383. https://doi.org/10.1128/jcm.05852-11

    Article  PubMed  PubMed Central  Google Scholar 

  18. Neugent ML, Hulyalkar NV, Nguyen VH, Zimmern PE, De Nisco NJ (2020) Advances in understanding the human urinary microbiome and its potential role in urinary tract infection. MBio 11:e00218-e220. https://doi.org/10.1128/mbio.00218-20

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214. https://doi.org/10.1038/nature1123

    Article  Google Scholar 

  20. NIH Human Microbiome Portfolio Analysis Team (2019) A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007–2016. Microbiome 7:31. https://doi.org/10.1186/s40168-019-0620-y

    Article  Google Scholar 

  21. Davis CD (2016) The gut microbiome and its role in obesity. Nutr Today 51:167–174. https://doi.org/10.1097/nt.0000000000000167

    Article  PubMed  PubMed Central  Google Scholar 

  22. Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E (2017) Dysbiosis and the immune system. Nat Rev Immunol 17:219–232. https://doi.org/10.1038/nri.2017.7

    Article  CAS  PubMed  Google Scholar 

  23. Sood U, Bajaj A, Kumar R, Khurana S, Kalia VC (2018) Infection and microbiome: impact of tuberculosis on human gut microbiome of Indian cohort. Indian J Microbiol 58:123–125. https://doi.org/10.1007/s12088-018-0706-4

    Article  PubMed  PubMed Central  Google Scholar 

  24. Rishi P, Thakur K, Vij S, Rishi L, Singh A, Kaur IP, Patel SK, Lee JK, Kalia VC (2020) Diet, gut microbiota and COVID-19. Indian J Microbiol 60:1–10. https://doi.org/10.1007/s12088-020-00908-0

    Article  CAS  Google Scholar 

  25. Tiffany CR, Bäumler AJ (2019) Dysbiosis: from fiction to function. Am J Physiol Gastrointest Liver Physiol 317:G602–G608. https://doi.org/10.1152/ajpgi.00230.2019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Cockwell P, Fisher LA (2020) The global burden of chronic kidney disease. Lancet 395:662–664. https://doi.org/10.1016/S0140-6736(19)32977-0

    Article  PubMed  Google Scholar 

  27. Girndt M (2017) Diagnosis and treatment of chronic kidney disease. Internist (Berl) 58:243–256. https://doi.org/10.1007/s00108-017-0195-2

    Article  CAS  Google Scholar 

  28. Lv JC, Zhang LX (2019) Prevalence and disease burden of chronic kidney disease. Adv Exp Med Biol 1165:3–15. https://doi.org/10.1007/978-981-13-8871-2_1

    Article  CAS  PubMed  Google Scholar 

  29. Alicic RZ, Rooney MT, Tuttle KR (2017) Diabetic kidney disease: challenges, progress, and possibilities. Clin J Am Soc Nephrol 12:2032–2045. https://doi.org/10.2215/cjn.11491116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Shankar M, Shashikala Narasimhappa MN (2021) Urinary tract infection in chronic kidney disease population: a clinical observational study. Cureus 13:e12486. https://doi.org/10.7759/cureus.12486

    Article  PubMed  PubMed Central  Google Scholar 

  31. Foxman B (2014) Urinary tract infection syndromes: occurrence, recurrence, bacteriology, risk factors, and disease burden. Infect Dis Clin North Am 28:1–3. https://doi.org/10.1016/j.idc.2013.09.003

    Article  PubMed  Google Scholar 

  32. Wang TZ, Kodiyanplakkal RP, Calfee DP (2019) Antimicrobial resistance in nephrology. Nat Rev Nephrol 15:463–481. https://doi.org/10.1038/s41581-019-0150-7

    Article  PubMed  PubMed Central  Google Scholar 

  33. Su G, Xu H, Riggi E, He Z, Lu L, Lindholm B, Marrone G, Wen Z, Liu X, Johnson DW, Carrero JJ (2018) Association of kidney function with infections by multidrug-resistant organisms: an electronic medical record analysis. Sci Rep 8:13372. https://doi.org/10.1038/s41598-018-31612-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Pietrucha-Dilanchian P, Hooton TM (2016) Diagnosis, treatment, and prevention of urinary tract infection. Microbiol Spectr. https://doi.org/10.1128/microbiolspec.uti-0021-2015

    Article  PubMed  Google Scholar 

  35. McLellan LK, Hunstad DA (2016) Urinary tract infection: pathogenesis and outlook. Trends Mol Med 22:946–957. https://doi.org/10.1016/j.molmed.2016.09.003

    Article  PubMed  PubMed Central  Google Scholar 

  36. Beerepoot MA, ter Riet G, Nys S, van der Wal WM, de Borgie CA, de Reijke TM, Prins JM, Koeijers J, Verbon A, Stobberingh E, Geerlings SE (2012) Lactobacilli vs antibiotics to prevent urinary tract infections: a randomised, double-blind, noninferiority trial in postmenopausal women. Arch Intern Med 172:704–712. https://doi.org/10.1001/archinternmed.2012.777

    Article  CAS  PubMed  Google Scholar 

  37. Kramer H, Kuffel G, Thomas-White K, Wolfe AJ, Vellanki K, Leehey DJ, Bansal VK, Brubaker L, Flanigan R, Koval J, Wadhwa A (2018) Diversity of the midstream urine microbiome in adults with chronic kidney disease. Int Urol Nephrol 50:1123–1130. https://doi.org/10.1007/s11255-018-1860-7

    Article  PubMed  PubMed Central  Google Scholar 

  38. Lecamwasam AR, Mohebbi M, Ekinci EI, Dwyer KM, Saffery R (2020) Identification of potential biomarkers of chronic kidney disease in individuals with diabetes: protocol for a cross-sectional observational study. JMIR Res Protoc 9:e16277. https://doi.org/10.2196/16277

    Article  PubMed  PubMed Central  Google Scholar 

  39. Liu F, Zhang N, Jiang P, Zhai Q, Li C, Yu D, Wu Y, Zhang Y, Lv L, Xu X, Feng N (2020) Characteristics of the urinary microbiome in kidney stone patients with hypertension. J Transl Med 18:130. https://doi.org/10.1186/s12967-020-02282-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Liu F, Ling Z, Xiao Y, Yang Q, Wang B, Zheng L, Jiang P, Li L, Wang W (2017) Alterations of urinary microbiota in type 2 diabetes mellitus with hypertension and/or hyperlipidemia. Front Pysiol 8:126. https://doi.org/10.3389/fphys.2017.00126

    Article  Google Scholar 

  41. Govender Y, Gabriel I, Minassian V, Fichorova R (2019) The current evidence on the association between the urinary microbiome and urinary incontinence in women. Front Cell Infect Microbiol 9:133. https://doi.org/10.3389/fcimb.2019.00133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Whiteside SA, Razvi H, Dave S, Reid G, Burton JP (2015) The microbiome of the urinary tract—a role beyond infection. Nat Rev Urol 12:81–90. https://doi.org/10.1038/nrurol.2014.361

    Article  PubMed  Google Scholar 

  43. Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8:51. https://doi.org/10.1186/s13073-016-0307-y

    Article  PubMed  PubMed Central  Google Scholar 

  44. Shafquat A, Joice R, Simmons SL, Huttenhower C (2014) Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol 22:261–266. https://doi.org/10.1016/j.tim.2014.01.011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Ekanayake A, Madegedara D, Chandrasekharan V, Magana-Arachchi D (2020) Respiratory bacterial microbiota and individual bacterial variability in lung cancer and bronchiectasis patients. Indian J Microbiol 60:196–205. https://doi.org/10.1007/s12088-019-00850-w

    Article  PubMed  Google Scholar 

  46. Huffnagle GB, Dickson RP, Lukacs NW (2017) The respiratory tract microbiome and lung inflammation: a two-way street. Mucosal Immunol 10:299–306. https://doi.org/10.1038/mi.2016.108

    Article  CAS  PubMed  Google Scholar 

  47. Tang J (2017) Microbiome in the urinary system—a review. AIMS Microbiol 3:143–154. https://doi.org/10.3934/microbiol.2017.2.143

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Meštrović T, Matijašić M, Perić M, Čipčić Paljetak H, Barešić A, Verbanac D (2020) The role of gut, vaginal, and urinary microbiome in urinary tract infections: from bench to bedside. Diagnostics (Basel) 11:7. https://doi.org/10.3390/diagnostics11010007

    Article  Google Scholar 

  49. Magruder M, Sholi AN, Gong C, Zhang L, Edusei E, Huang J, Albakry S, Satlin MJ, Westblade LF, Crawford C, Dadhania DM (2019) Gut uropathogen abundance is a risk factor for development of bacteriuria and urinary tract infection. Nat Commun 10:1–9. https://doi.org/10.1038/s41467-019-13467-w

    Article  CAS  Google Scholar 

  50. Pohl HG, Groah SL, Pérez-Losada M, Ljungberg I, Sprague BM, Chandal N, Caldovic L, Hsieh M (2020) The urine microbiome of healthy men and women differs by urine collection method. Int Neurourol J 24:41–51. https://doi.org/10.5213/inj.1938244.122

    Article  PubMed  PubMed Central  Google Scholar 

  51. Lewis DA, Brown R, Williams J, White P, Jacobson SK, Marchesi J, Drake MJ (2013) The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol 3:41. https://doi.org/10.3389/fcimb.2013.00041

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Sommariva M, Le Noci V, Bianchi F, Camelliti S, Balsari A, Tagliabue E, Sfondrini L (2020) The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy. Cell Mol Life Sci 77:2739–2749. https://doi.org/10.1007/s00018-020-03452-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Popović VB, Šitum M, Chow CE, Chan LS, Roje B, Terzić J (2018) The urinary microbiome associated with bladder cancer. Sci Rep 8:12157. https://doi.org/10.1038/s41598-018-29054-w

    Article  CAS  Google Scholar 

  54. Wojciuk B, Salabura A, Grygorcewicz B, Kędzierska K, Ciechanowski K, Dołęgowska B (2019) Urobiome: in sickness and in health. Microorganisms 7:548. https://doi.org/10.3390/microorganisms7110548

    Article  CAS  PubMed Central  Google Scholar 

  55. Iizumi T, Battaglia T, Ruiz V, Perez GI (2017) Gut microbiome and antibiotics. Arch Med Res 48:727–734. https://doi.org/10.1016/j.arcmed.2017.11.004

    Article  CAS  PubMed  Google Scholar 

  56. Mulder M, Radjabzadeh D, Hassing RJ, Heeringa J, Uitterlinden AG, Kraaij R, Stricker BH, Verbon A (2019) The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC Microbiol 19:1–7. https://doi.org/10.1186/s12866-018-1379-1

    Article  Google Scholar 

  57. Ceprnja M, Oros D, Melvan E, Svetlicic E, Skrlin J, Barisic K, Starcevic L, Zucko J, Starcevic A (2021) Modeling of urinary microbiota associated with cystitis. Front Cell Infect Microbiol 11:643638. https://doi.org/10.3389/fcimb.2021.643638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Llor C, Bjerrum L (2014) Antimicrobial resistance: risk associated with antibiotic overuse and initiatives to reduce the problem. Ther Adv Drug Saf 5:229–241. https://doi.org/10.1177/2042098614554919

    Article  PubMed  PubMed Central  Google Scholar 

  59. Cumpanas AA, Bratu OG, Bardan RT, Ferician OC, Cumpanas AD, Horhat FG, Licker M, Pricop C, Cretu OM (2020) Urinary microbiota—are we ready for prime time? a literature review of study methods’ critical steps in avoiding contamination and minimising biased results. Diagnostics (Basel) 10:343. https://doi.org/10.3390/diagnostics10060343

    Article  CAS  Google Scholar 

  60. Karstens L, Asquith M, Caruso V, Rosenbaum JT, Fair DA, Braun J, Gregory WT, Nardos R, McWeeney SK (2018) Community profiling of the urinary microbiota: considerations for low-biomass samples. Nat Rev Urol 15:735–749. https://doi.org/10.1038/s41585-018-0104-z

    Article  PubMed  PubMed Central  Google Scholar 

  61. Chen J, Zhao J, Cao Y, Zhang G, Chen Y, Zhong J, Huang W, Zeng J, Wu P (2019) Relationship between alterations of urinary microbiota and cultured negative lower urinary tract symptoms in female type 2 diabetes patients. BMC Urol 19:78. https://doi.org/10.1186/s12894-019-0506-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Rivers B, Steck TR (2001) Viable but nonculturable uropathogenic bacteria are present in the mouse urinary tract following urinary tract infection and antibiotic therapy. Urol Res 29:60–66. https://doi.org/10.1007/s002400000151

    Article  CAS  PubMed  Google Scholar 

  63. Hooks KB, O’Malley MA (2017) Dysbiosis and its discontents. MBio 8:e01492-e1517. https://doi.org/10.1128/mbio.01492-17

    Article  PubMed  PubMed Central  Google Scholar 

  64. Grine G, Lotte R, Chirio D, Chevalier A, Raoult D, Drancourt M, Ruimy R (2019) Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection. EBioMedicine 43:333–337. https://doi.org/10.1016/j.ebiom.2019.04.037

    Article  PubMed  PubMed Central  Google Scholar 

  65. Kim Y, Carrai M, Leung MH, Chin J, Li J, Lee PK, Beatty JA, Pfeiffer DU, Barrs VR (2021) Dysbiosis of the urinary bladder microbiome in cats with chronic kidney disease. mSystems 6:e0051021. https://doi.org/10.1128/msystems.00510-21

    Article  CAS  PubMed  Google Scholar 

  66. Ling Z, Liu F, Shao L, Cheng Y, Li L (2017) Dysbiosis of the urinary microbiota associated with urine levels of proinflammatory chemokine interleukin-8 in female type 2 diabetic patients. Front Immunol 8:1032. https://doi.org/10.3389/fimmu.2017.01032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Liu F, Ling Z, Xiao Y, Lv L, Yang Q, Wang B, Lu H, Zheng L, Jiang P, Wang W, Li L (2017) Dysbiosis of urinary microbiota is positively correlated with type 2 diabetes mellitus. Oncotarget 8:3798–3810. https://doi.org/10.18632/oncotarget.14028

    Article  PubMed  Google Scholar 

  68. Nickel JC (2007) Urinary tract infections and resistant bacteria: highlights of a symposium at the combined meeting of the 25th international congress of chemotherapy (icc) and the 17th European congress of clinical microbiology and infectious diseases (eccmid), March 31–April 3, 2007, Munich, Germany. Rev Urol 9:78–80

    PubMed  PubMed Central  Google Scholar 

  69. Thänert R, Reske KA, Hink T, Wallace MA, Wang B, Schwartz DJ, Seiler S, Cass C, Burnham CA, Dubberke ER, Kwon JH (2019) Comparative genomics of antibiotic-resistant uropathogens implicates three routes for recurrence of urinary tract infections. mBbio 10:e01977-e2019. https://doi.org/10.1128/mbio.01977-19

    Article  CAS  Google Scholar 

  70. Naber KG, Kogan M, Wagenlehner FM, Siener R, Gessner A (2017) How the microbiome is influenced by the therapy of urological diseases: standard versus alternative approaches. Clinical Phytoscience 3:1–4. https://doi.org/10.1186/s40816-017-0045-8

    Article  CAS  Google Scholar 

  71. Moustafa A, Li W, Singh H, Moncera KJ, Torralba MG, Yu Y, Manuel O, Biggs W, Venter JC, Nelson KE, Pieper R (2018) Microbial metagenome of urinary tract infection. Sci Rep 8:4333. https://doi.org/10.1038/s41598-018-22660-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Gaston JR, Johnson AO, Bair KL, White AN, Armbruster CE (2021) Polymicrobial interactions in the urinary tract: is the enemy of my enemy my friend?.Infect and Immun IAI.00652–20. https://doi.org/10.1128/iai.00652-20

  73. Thomas S, Dunn CD, Campbell LJ, Strand DW, Vezina CM, Bjorling DE, Penniston KL, Li L, Ricke WA, Goldberg TL (2021) A multi-omic investigation of male lower urinary tract symptoms: potential role for JC virus. PLoS ONE 16:e0246266. https://doi.org/10.1371/journal.pone.0246266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Burnett LA, Hochstedler BR, Weldon K, Wolfe AJ, Brubaker L (2021) Recurrent urinary tract infection: association of clinical profiles with urobiome composition in women. Neurourol Urodyn 40:1479–1489. https://doi.org/10.1002/nau.24707

    Article  CAS  PubMed  Google Scholar 

  75. Horwitz D, McCue T, Mapes AC, Ajami NJ, Petrosino JF, Ramig RF, Trautner BW (2015) Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference. J Infect 71:358–367. https://doi.org/10.1016/j.jinf.2015.05.014

    Article  PubMed  PubMed Central  Google Scholar 

  76. Thomas-White KJ, Gao X, Lin H, Fok CS, Ghanayem K, Mueller ER, Dong Q, Brubaker L, Wolfe AJ (2018) Urinary microbes and postoperative urinary tract infection risk in urogynecologic surgical patients. Int Urogynecol J 29:1797–1805. https://doi.org/10.1007/s00192-018-3767-3

    Article  PubMed  PubMed Central  Google Scholar 

  77. Nienhouse V, Gao X, Dong Q, Nelson DE, Toh E, McKinley K, Schreckenberger P, Shibata N, Fok CS, Mueller ER, Brubaker L (2014) Interplay between bladder microbiota and urinary antimicrobial peptides: mechanisms for human urinary tract infection risk and symptom severity. PLoS ONE 9:e114185. https://doi.org/10.1371/journal.pone.0114185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kumar R, Sood U, Gupta V, Singh M, Scaria J, Lal R (2020) Recent advancements in the development of modern probiotics for restoring human gut microbiome dysbiosis. Indian J Microbiol 60:12–25. https://doi.org/10.1007/s12088-019-00808-y

    Article  CAS  PubMed  Google Scholar 

  79. Rudick CN, Taylor AK, Yaggie RE, Schaeffer AJ, Klumpp DJ (2014) Asymptomatic bacteriuria Escherichia coli are live biotherapeutics for UTI. PLoS ONE 9:e109321. https://doi.org/10.1371/journal.pone.0109321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Pierre JF, Akbilgic O, Smallwood H, Cao X, Fitzpatrick EA, Pena S, Furmanek SP, Ramirez JA, Jonsson CB (2020) Discovery and predictive modeling of urine microbiome, metabolite and cytokine biomarkers in hospitalised patients with community acquired pneumonia. Sci Rep 10:13418. https://doi.org/10.1038/s41598-020-70461-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Bi H, Tian Y, Song C, Li J, Liu T, Chen Z, Chen C, Huang Y, Zhang Y (2019) Urinary microbiota–a potential biomarker and therapeutic target for bladder cancer. J Med Microbiol 68:1471–1478. https://doi.org/10.1099/jmm.0.001058

    Article  CAS  PubMed  Google Scholar 

  82. Choi Y, Park HS, Jee YK (2021) Urine microbial extracellular vesicles can be potential and novel biomarkers for allergic diseases. Allergy Asthma Immunol Res 13:5–7. https://doi.org/10.4168/aair.2021.13.1.5

    Article  CAS  PubMed  Google Scholar 

  83. Lee HJ (2019) Microbe-host communication by small RNAs in extracellular vesicles: vehicles for transkingdom RNA transportation. Int J Mol Sci 20:1487. https://doi.org/10.3390/ijms20061487

    Article  CAS  PubMed Central  Google Scholar 

  84. Gupta K, Stapleton AE, Hooton TM, Roberts PL, Fennell CL, Stamm WE (1998) Inverse association of H2O2-producing lactobacilli and vaginal Escherichia coli colonisation in women with recurrent urinary tract infections. J Infect Dis 178:446–450. https://doi.org/10.1086/515635

    Article  CAS  PubMed  Google Scholar 

  85. Wong AC, Levy M (2019) New approaches to microbiome-based therapies. mSystems 4:e00122-e219. https://doi.org/10.1128/msystems.00122-19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Bajic P, Wolfe AJ, Gupta GN (2019) Old instillations and new implications for bladder cancer: the urinary microbiome and intravesical BCG. BJU Int 124:7–8. https://doi.org/10.1111/bju.14683

    Article  PubMed  Google Scholar 

  87. Aragon IM, Herrera-Imbroda B, Queipo-Ortuño MI, Castillo E, Del Moral JS, Gomez-Millan J, Yucel G, Lara MF (2018) The urinary tract microbiome in health and disease. Eur Urol Focus 4:128–138. https://doi.org/10.1016/j.euf.2016.11.001

    Article  PubMed  Google Scholar 

  88. Xu H, Tamrat NE, Gao J, Xu J, Zhou Y, Zhang S, Chen Z, Shao Y, Ding L, Shen B, Wei Z (2021) Combined signature of the urinary microbiome and metabolome in patients with interstitial cystitis. Front Cell Infect Microbiol 11:711746. https://doi.org/10.3389/fcimb.2021.711746

    Article  PubMed  PubMed Central  Google Scholar 

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  1. Molecular Microbiology and Human Diseases Project, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka

    Shehani Jayalath & Dhammika Magana-Arachchi

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  1. Shehani Jayalath
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  2. Dhammika Magana-Arachchi
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Correspondence to Dhammika Magana-Arachchi.

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Jayalath, S., Magana-Arachchi, D. Dysbiosis of the Human Urinary Microbiome and its Association to Diseases Affecting the Urinary System. Indian J Microbiol 62, 153–166 (2022). https://doi.org/10.1007/s12088-021-00991-x

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