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The Bladder is Not Sterile: an Update on the Urinary Microbiome

  • Overactive Bladder (U Lee and S Adelstein, Section Editors)
  • Published:
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Abstract

Purpose of Review

The article discusses (1) techniques used to study bacterial urinary microbiota; (2) existence of non-bacterial urinary microbiota; (3) associations between changes in urinary microbiota and various benign lower urinary tract disorders.

Recent Findings

Urine harbors a diverse microbial community that resides within it. A multitude of studies have identified differences in these communities associated with urologic conditions, suggesting that microbial communities may maintain normal bladder homeostasis. Technological advances in analytic approaches have improved our understanding of the urinary microbiome. The choice of urine sampling method (voided, catheterized, or aspirated) will significantly influence microbiome findings. Sex and age highly influence urinary microbiota; in addition to rigorous inclusion criteria, microbial studies must be sufficiently powered to overcome the substantial interindividual variability of urinary microbiota. Regardless of these complicating factors, studies have identified microbial patterns correlating with both urologic diagnoses and treatment responses.

Summary

Without a clear understanding of the variability of and exogenous influences on the urinary microbiota in the absence of disease, it has been challenging to reveal the microbial patterns responsible for disease pathophysiology. Host mechanisms in response to the urinary microbiome are also poorly understood. Additional research can address whether the manipulation of urinary microbiota will benefit lower urinary tract health.

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References

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

  1. Whiteside SA, Razvi H, Dave S, Reid G, Burton JP. The microbiome of the urinary tract--a role beyond infection. Nat Rev Urol. 2015;12(2):81–90. https://doi.org/10.1038/nrurol.2014.361.

    Article  PubMed  Google Scholar 

  2. Thomas-White K, Brady M, Wolfe AJ, Mueller ER. The bladder is not sterile: history and current discoveries on the urinary microbiome. Curr Bladder Dysfunct Rep. 2016;11(1):18–24. https://doi.org/10.1007/s11884-016-0345-8.

    Article  PubMed  PubMed Central  Google Scholar 

  3. •• Karstens L, Asquith M, Caruso V, Rosenbaum JT, Fair DA, Braun J, et al. Community profiling of the urinary microbiota: considerations for low-biomass samples. Nat Rev Urol. 2018;15(12):735–49. https://doi.org/10.1038/s41585-018-0104-zThis is an in-depth exploration of the detailed decisions in the analysis of microbial sequence data that can influence the results and findings of microbiome studies of the urinary tract.

    Article  PubMed  PubMed Central  Google Scholar 

  4. • Wolfe AJ, Toh E, Shibata N, Rong R, Kenton K, Fitzgerald M, et al. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 2012;50(4):1376–83. https://doi.org/10.1128/JCM.05852-11One of the first descriptions of the presence of bacteria within the urinary tract; it is also the only study to detail the profound differences in microbial communities detected with different methods of sampling the urinary tract.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Ackerman AL, Khalique MU, Ackerman JE, Tang J, Kim J, Underhill DM et al. Optimization of DNA extraction from human urinary samples for mycobiome community profiling. PLoS One. 2019;14(4).

    Article  CAS  Google Scholar 

  6. Caruso V, Song X, Asquith M, Karstens L. Performance of microbiome sequence inference methods in environments with varying biomass. mSystems. 2019;4(1). doi:https://doi.org/10.1128/mSystems.00163-18.

  7. Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog. 2010;6(1):e1000713. https://doi.org/10.1371/journal.ppat.1000713.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, et al. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol. 2012;13(7):R60. https://doi.org/10.1186/gb-2012-13-7-r60.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, Bittinger K, et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 2010;10:206. https://doi.org/10.1186/1471-2180-10-206.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One. 2012;7(3):e33865. https://doi.org/10.1371/journal.pone.0033865.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Bao Y, Al KF, Chanyi RM, Whiteside S, Dewar M, Razvi H, et al. Questions and challenges associated with studying the microbiome of the urinary tract. Ann Transl Med. 2017;5(2):33. https://doi.org/10.21037/atm.2016.12.14.

    Article  Google Scholar 

  12. Earl JP, Adappa ND, Krol J, Bhat AS, Balashov S, Ehrlich RL, et al. Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. Microbiome. 2018;6(1):190. https://doi.org/10.1186/s40168-018-0569-2.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Sianou A, Galyfos G, Kaparos G. Re: Alan J. Wolfe, Linda Brubaker. “Sterile urine” and the presence of bacteria. Eur Urol 2015;68:173-4. Eur Urol. 2016;69(1):e7. doi:https://doi.org/10.1016/j.eururo.2015.06.052.

    Article  Google Scholar 

  14. Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol. 2002;68(7):3401–7. https://doi.org/10.1128/aem.68.7.3401-3407.2002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Momozawa Y, Deffontaine V, Louis E, Medrano JF. Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human. PLoS One. 2011;6(2):e16952. https://doi.org/10.1371/journal.pone.0016952.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. •• Thomas-White K, Forster SC, Kumar N, Van Kuiken M, Putonti C, Stares MD, et al. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nat Commun. 2018;9(1):1557. https://doi.org/10.1038/s41467-018-03968-5Cross-sectional sampling of the urogenital tract in a cohort of female patients reveals strong interrelationship between the vaginal and urinary microbiome that may suggest an interconnected urogenital microbiome, at least in women.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Liu F, Ling Z, Xiao Y, Lv L, Yang Q, Wang B, et al. Dysbiosis of urinary microbiota is positively correlated with type 2 diabetes mellitus. Oncotarget. 2017;8(3):3798–810. https://doi.org/10.18632/oncotarget.14028.

    Article  PubMed  Google Scholar 

  18. Rani A, Ranjan R, McGee HS, Andropolis KE, Panchal DV, Hajjiri Z, et al. Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance. Transl Res. 2017;181:59–70. https://doi.org/10.1016/j.trsl.2016.08.008.

    Article  CAS  Google Scholar 

  19. Karstens L, Asquith M, Davin S, Stauffer P, Fair D, Gregory WT, et al. Does the urinary microbiome play a role in urgency urinary incontinence and its severity? Front Cell Infect Microbiol. 2016;6:78. https://doi.org/10.3389/fcimb.2016.00078.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. • Thomas-White KJ, Hilt EE, Fok C, Pearce MM, Mueller ER, Kliethermes S, et al. Incontinence medication response relates to the female urinary microbiota. Int Urogynecol J. 2016;27(5):723–33. https://doi.org/10.1007/s00192-015-2847-xThe baseline urinary microbiome prior to treatment in a population of women with UUI was related to medication responses, providing the first evidence that the urinary microbiome may be a useful prognostic biomarker in the classification of patients with benign urologic conditions.

    Article  PubMed  Google Scholar 

  21. Shoskes DA, Altemus J, Polackwich AS, Tucky B, Wang H, Eng C. The urinary microbiome differs significantly between patients with chronic prostatitis/chronic pelvic pain syndrome and controls as well as between patients with different clinical phenotypes. Urology. 2016;92:26–32. https://doi.org/10.1016/j.urology.2016.02.043.

    Article  PubMed  Google Scholar 

  22. • Abernethy MG, Rosenfeld A, White JR, Mueller MG, Lewicky-Gaupp C, Kenton K. Urinary microbiome and cytokine levels in women with interstitial cystitis. Obstet Gynecol. 2017;129(3):500–6. https://doi.org/10.1097/AOG.0000000000001892This small study of a cohort of women with interstitial cystitis and age-matched controls identified alterations in the microbiome that also correlated with both increased inflammatory cytokine levels and worsening symptom scores, suggesting a functional consequence associated with shifts in urogenital microbial communities.

    Article  CAS  Google Scholar 

  23. Kramer H, Kuffel G, Thomas-White K, Wolfe AJ, Vellanki K, Leehey DJ, et al. Diversity of the midstream urine microbiome in adults with chronic kidney disease. Int Urol Nephrol. 2018;50(6):1123–30. https://doi.org/10.1007/s11255-018-1860-7.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Wu P, Chen Y, Zhao J, Zhang G, Chen J, Wang J, et al. Urinary microbiome and psychological factors in women with overactive bladder. Front Cell Infect Microbiol. 2017;7:488. https://doi.org/10.3389/fcimb.2017.00488.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Curtiss N, Balachandran A, Krska L, Peppiatt-Wildman C, Wildman S, Duckett J. Age, menopausal status and the bladder microbiome. Eur J Obstet Gynecol Reprod Biol. 2018;228:126–9. https://doi.org/10.1016/j.ejogrb.2018.06.011.

    Article  PubMed  Google Scholar 

  26. Komesu YM, Richter HE, Carper B, Dinwiddie DL, Lukacz ES, Siddiqui NY, et al. The urinary microbiome in women with mixed urinary incontinence compared to similarly aged controls. Int Urogynecol J. 2018;29(12):1785–95. https://doi.org/10.1007/s00192-018-3683-6.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Komesu YM, Richter HE, Dinwiddie DL, Siddiqui NY, Sung VW, Lukacz ES, et al. Methodology for a vaginal and urinary microbiome study in women with mixed urinary incontinence. Int Urogynecol J. 2017;28(5):711–20. https://doi.org/10.1007/s00192-016-3165-7.

    Article  PubMed  Google Scholar 

  28. Liu F, Ling Z, Xiao Y, Yang Q, Zheng L, Jiang P, et al. Characterization of the urinary microbiota of elderly women and the effects of type 2 diabetes and urinary tract infections on the microbiota. Oncotarget. 2017;8(59):100678–90. https://doi.org/10.18632/oncotarget.21126.

    Article  PubMed  PubMed Central  Google Scholar 

  29. Hassall A. On the development of torulae in the urine, and on the relation of these fungi to albuminous and saccharine urine. Med Chir Trans. 1853;36:23–78 9. https://doi.org/10.1177/095952875303600103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K, Fok C, et al. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. mBio. 2014;5(4):e01283–14. https://doi.org/10.1128/mBio.01283-14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. • Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ, Mueller ER, 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):871–6. https://doi.org/10.1128/JCM.02876-13This paper describes the use of an enhanced culture technique to show that multiple genera of bacteria are culturable from urine obtained by catheterization from asymptomatic women.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S, Brincat C, et al. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol. 2016;54(5):1216–22. https://doi.org/10.1128/JCM.00044-16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Nickel JC, Stephens A, Landis JR, Mullins C, van Bokhoven A, Anger JT, et al. Urinary fungi associated with urinary symptom severity among women with interstitial cystitis/bladder pain syndrome (IC/BPS). World J Urol. 2019. https://doi.org/10.1007/s00345-019-02764-0.

  34. • Nickel JC, Stephens A, Landis JR, Mullins C, van Bokhoven A, Lucia MS, et al. Assessment of the lower urinary tract microbiota during symptom flare in women with urologic chronic pelvic pain syndrome: a MAPP network study. J Urol. 2016;195(2):356–62. https://doi.org/10.1016/j.juro.2015.09.075In a large cohort of patients with urologic chronic pelvic pain syndrome, an association of worsening symptoms, dubbed symptomatic “flares”, was associated with increased detection of urinary fungi, revealing an importance for non-bacterial organisms in disease is is being increasingly recognized for other organ systems.

    Article  PubMed  Google Scholar 

  35. Ackerman AL, Underhill DM. The mycobiome of the human urinary tract: potential roles for fungi in urology. Ann Transl Med. 2017;5(2):31. https://doi.org/10.21037/atm.2016.12.69.

    Article  Google Scholar 

  36. Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, et al. Immunological consequences of intestinal fungal dysbiosis. Cell Host Microbe. 2016;19(6):865–73. https://doi.org/10.1016/j.chom.2016.05.003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. El-Jurdi N, Ghannoum MA. The mycobiome: impact on health and disease states. Microbiol Spectr. 2017;5(3). doi:https://doi.org/10.1128/microbiolspec.FUNK-0045-2016.

  38. Santiago-Rodriguez TM. Identification and quantification of DNA viral populations in human urine using next-generation sequencing approaches. Methods Mol Biol. 1838;2018:191–200. https://doi.org/10.1007/978-1-4939-8682-8_14.

    Article  CAS  Google Scholar 

  39. Santiago-Rodriguez TM, Ly M, Bonilla N, Pride DT. The human urine virome in association with urinary tract infections. Front Microbiol. 2015;6:14. https://doi.org/10.3389/fmicb.2015.00014.

    Article  PubMed  PubMed Central  Google Scholar 

  40. Divers J, Langefeld CD, Lyles DS, Ma L, Freedman BI. Protective association between JC polyoma viruria and kidney disease. Curr Opin Nephrol Hypertens. 2019;28(1):65–9. https://doi.org/10.1097/MNH.0000000000000464.

    Article  PubMed  Google Scholar 

  41. Rani A, Ranjan R, McGee HS, Metwally A, Hajjiri Z, Brennan DC, et al. A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms. Sci Rep. 2016;6:33327. https://doi.org/10.1038/srep33327.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Garretto A, Thomas-White K, Wolfe AJ, Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virol. 2018;99(8):1141–6. https://doi.org/10.1099/jgv.0.001097.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Sigdel TK, Mercer N, Nandoe S, Nicora CD, Burnum-Johnson K, Qian WJ, et al. Urinary virome perturbations in kidney transplantation. Front Med (Lausanne). 2018;5:72. https://doi.org/10.3389/fmed.2018.00072.

    Article  Google Scholar 

  44. Garretto A, Miller-Ensminger T, Wolfe AJ, Putonti C. Bacteriophages of the lower urinary tract. Nat Rev Urol. 2019;16(7):422–32. https://doi.org/10.1038/s41585-019-0192-4.

    Article  PubMed  Google Scholar 

  45. Malki K, Shapiro JW, Price TK, Hilt EE, Thomas-White K, Sircar T, et al. Genomes of Gardnerella strains reveal an abundance of prophages within the bladder microbiome. PLoS One. 2016;11(11):e0166757. https://doi.org/10.1371/journal.pone.0166757.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. • Miller-Ensminger T, Garretto A, Brenner J, Thomas-White K, Zambom A, Wolfe AJ et al. Bacteriophages of the urinary microbiome. J Bacteriol. 2018;200(7). doi:https://doi.org/10.1128/JB.00738-17. This study provides early evidence of the existence of abundant and novel bacteriophages within the urinary tract that likely influence both the composition of the urinary microbiome as well as urologic disease.

  47. Ujmajuridze A, Chanishvili N, Goderdzishvili M, Leitner L, Mehnert U, Chkhotua A, et al. Adapted bacteriophages for treating urinary tract infections. Front Microbiol. 2018;9:1832. https://doi.org/10.3389/fmicb.2018.01832.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Nzakizwanayo J, Hanin A, Alves DR, McCutcheon B, Dedi C, Salvage J, et al. Bacteriophage can prevent encrustation and blockage of urinary catheters by Proteus mirabilis. Antimicrob Agents Chemother. 2015;60(3):1530–6. https://doi.org/10.1128/AAC.02685-15.

    Article  PubMed  Google Scholar 

  49. Coyne KS, Sexton CC, Thompson CL, Milsom I, Irwin D, Kopp ZS, et al. The prevalence of lower urinary tract symptoms (LUTS) in the USA, the UK and Sweden: results from the Epidemiology of LUTS (EpiLUTS) study. BJU Int. 2009;104(3):352–60. https://doi.org/10.1111/j.1464-410X.2009.08427.x.

    Article  PubMed  Google Scholar 

  50. Ackerman AL, Lai HH, Parameshwar PS, Eilber KS, Anger JT. Symptomatic overlap in overactive bladder and interstitial cystitis/painful bladder syndrome - development of a new algorithm. BJU Int. 2018. https://doi.org/10.1111/bju.14568.

    Article  Google Scholar 

  51. Thomas-White KJ, Kliethermes S, Rickey L, Lukacz ES, Richter HE, Moalli P, et al. Evaluation of the urinary microbiota of women with uncomplicated stress urinary incontinence. Am J Obstet Gynecol. 2017;216(1):55 e1–e16. https://doi.org/10.1016/j.ajog.2016.07.049.

    Article  Google Scholar 

  52. Fok CS, Gao X, Lin H, Thomas-White KJ, Mueller ER, Wolfe AJ, et al. Urinary symptoms are associated with certain urinary microbes in urogynecologic surgical patients. Int Urogynecol J. 2018;29(12):1765–71. https://doi.org/10.1007/s00192-018-3732-1.

    Article  PubMed  PubMed Central  Google Scholar 

  53. Pearce MM, Zilliox MJ, Rosenfeld AB, Thomas-White KJ, Richter HE, Nager CW, et al. The female urinary microbiome in urgency urinary incontinence. Am J Obstet Gynecol. 2015;213(3):347 e1–11. https://doi.org/10.1016/j.ajog.2015.07.009.

    Article  Google Scholar 

  54. Nickel JC, Stephens A, Landis JR, Chen J, Mullins C, van Bokhoven A, et al. Search for microorganisms in men with urologic chronic pelvic pain syndrome: a culture-independent analysis in the MAPP Research Network. J Urol. 2015;194(1):127–35. https://doi.org/10.1016/j.juro.2015.01.037.

    Article  PubMed  PubMed Central  Google Scholar 

  55. Bresler L, Price TK, Hilt EE, Joyce C, Fitzgerald CM, Wolfe AJ. Female lower urinary tract microbiota do not associate with IC/PBS symptoms: a case-controlled study. Int Urogynecol J. 2019. https://doi.org/10.1007/s00192-019-03942-9.

    Article  Google Scholar 

  56. Nickel JC, Stephens-Shields AJ, Landis JR, Mullins C, van Bokhoven A, Lucia MS et al. A culture-independent analysis of the microbiota of female interstitial cystitis/bladder pain syndrome participants in the MAPP Research Network. J Clin Med. 2019;8(3). doi:https://doi.org/10.3390/jcm8030415.

    Article  Google Scholar 

  57. Meriwether KV, Lei Z, Singh R, Gaskins J, DTG H. Jala V. The vaginal and urinary microbiomes in premenopausal women with interstitial cystitis/bladder pain syndrome as compared to unaffected controls: a pilot cross-sectional study. Front Cell Infect Microbiol. 2019;9:92. https://doi.org/10.3389/fcimb.2019.00092.

  58. Greenbaum S, Greenbaum G, Moran-Gilad J, Weintraub AY. Ecological dynamics of the vaginal microbiome in relation to health and disease. Am J Obstet Gynecol. 2019;220(4):324–35. https://doi.org/10.1016/j.ajog.2018.11.1089.

    Article  PubMed  Google Scholar 

  59. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4680–7. https://doi.org/10.1073/pnas.1002611107.

    Article  PubMed  Google Scholar 

  60. De Gregorio PR, Silva JA, Marchesi A, Nader-Macias MEF. Anti-Candida activity of beneficial vaginal lactobacilli in in vitro assays and in a murine experimental model. FEMS Yeast Res. 2019;19(2). doi:https://doi.org/10.1093/femsyr/foz008.

  61. Jang SJ, Lee K, Kwon B, You HJ, Ko G. Vaginal lactobacilli inhibit growth and hyphae formation of Candida albicans. Sci Rep. 2019;9(1):8121. https://doi.org/10.1038/s41598-019-44579-4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Finucane TE. ‘Urinary tract infection’ and the microbiome. Am J Med. 2017;130(3):e97–e8. https://doi.org/10.1016/j.amjmed.2016.08.018.

    Article  PubMed  Google Scholar 

  63. Anger J, Lee U, Ackerman AL, Chou R, Chughtai B, Clemens JQ et al. Recurrent uncomplicated urinary tract infections in women: AUA/CUA/SUFU Guideline. J Urol. 2019:101097JU0000000000000296. doi:https://doi.org/10.1097/JU.0000000000000296.

    Article  Google Scholar 

  64. Price TK, Hilt EE, Dune TJ, Mueller ER, Wolfe AJ, Brubaker L. Urine trouble: should we think differently about UTI? Int Urogynecol J. 2018;29(2):205–10. https://doi.org/10.1007/s00192-017-3528-8.

    Article  PubMed  Google Scholar 

  65. Cai T, Mazzoli S, Mondaini N, Meacci F, Nesi G, D'Elia C, et al. The role of asymptomatic bacteriuria in young women with recurrent urinary tract infections: to treat or not to treat? Clin Infect Dis. 2012;55(6):771–7. https://doi.org/10.1093/cid/cis534.

    Article  PubMed  Google Scholar 

  66. Roos V, Ulett GC, Schembri MA, Klemm P. The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine. Infect Immun. 2006;74(1):615–24. https://doi.org/10.1128/IAI.74.1.615-624.2006.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Stork C, Kovacs B, Rozsai B, Putze J, Kiel M, Dorn A, et al. Characterization of asymptomatic bacteriuria Escherichia coli isolates in search of alternative strains for efficient bacterial interference against uropathogens. Front Microbiol. 2018;9:214. https://doi.org/10.3389/fmicb.2018.00214.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Ohlemacher SI, Giblin DE, d’Avignon DA, Stapleton AE, Trautner BW, Henderson JP. Enterobacteria secrete an inhibitor of Pseudomonas virulence during clinical bacteriuria. J Clin Invest. 2017;127(11):4018–30. https://doi.org/10.1172/JCI92464.

    Article  PubMed  PubMed Central  Google Scholar 

  69. •• Schreiber HLt, Conover MS, Chou WC, Hibbing ME, Manson AL, Dodson KW et al. Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections. Sci Transl Med. 2017;9(382). doi:https://doi.org/10.1126/scitranslmed.aaf1283. This comparative genomic study examining a panel of E. coli isolates from women with urinary tract infections revealed conserved functional, but not genomic, virulence patterns at the bacterial strain level, suggesting important host-pathogen interactions at the root of infection susceptibility.

    Article  Google Scholar 

  70. Krieger JN, Thumbikat P. Bacterial Prostatitis: Bacterial Virulence, Clinical outcomes, and new directions. Microbiol Spectr. 2016;4(1). doi:https://doi.org/10.1128/microbiolspec.UTI-0004-2012.

  71. Tchesnokova V, Avagyan H, Rechkina E, Chan D, Muradova M, Haile HG, et al. Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection. PLoS One. 2017;12(3):e0174132. https://doi.org/10.1371/journal.pone.0174132.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Dune TJ, Price TK, Hilt EE, Thomas-White KJ, Kliethermes S, Brincat C, et al. Urinary symptoms and their associations with urinary tract infections in urogynecologic patients. Obstet Gynecol. 2017;130(4):718–25. https://doi.org/10.1097/AOG.0000000000002239.

    Article  PubMed  PubMed Central  Google Scholar 

  73. Stapleton AE. The vaginal microbiota and urinary tract infection. Microbiol Spectr. 2016;4(6). doi:https://doi.org/10.1128/microbiolspec.UTI-0025-2016.

  74. • Gilbert NM, O'Brien VP, Lewis AL. Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease. PLoS Pathog. 2017;13(3):e1006238. https://doi.org/10.1371/journal.ppat.1006238In mice primed for recurrent urinary tract infections, intraurethral innoculation of Gardnerella, a bacterium associated in humans with bacterial vaginosis, can promote the development of E. coli urinary tract infection, suggesting that infection risk is a complex interplay not only between host and pathogen but that the microbial environment can also promote infection.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4554–61. https://doi.org/10.1073/pnas.1000087107.

    Article  Google Scholar 

  76. Kohler O, Petersen L, Mors O, Mortensen PB, Yolken RH, Gasse C, et al. Infections and exposure to anti-infective agents and the risk of severe mental disorders: a nationwide study. Acta Psychiatr Scand. 2017;135(2):97–105. https://doi.org/10.1111/acps.12671.

    Article  CAS  PubMed  Google Scholar 

  77. Kohler-Forsberg O, Petersen L, Gasse C, Mortensen PB, Dalsgaard S, Yolken RH, et al. A nationwide study in denmark of the association between treated infections and the subsequent risk of treated mental disorders in children and adolescents. JAMA Psychiatry. 2018. https://doi.org/10.1001/jamapsychiatry.2018.3428.

    Article  Google Scholar 

  78. Noverr MC, Falkowski NR, McDonald RA, McKenzie AN, Huffnagle GB. Development of allergic airway disease in mice following antibiotic therapy and fungal microbiota increase: role of host genetics, antigen, and interleukin-13. Infect Immun. 2005;73(1):30–8. https://doi.org/10.1128/IAI.73.1.30-38.2005.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. • Mulder M, Radjabzadeh D, Hassing RJ, Heeringa J, Uitterlinden AG, Kraaij R, et al. The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population. BMC Microbiol. 2019;19(1):9. https://doi.org/10.1186/s12866-018-1379-1Despite widespread use of antibiotics to treat uropathogens such as E. coli, this examination of older adults after treatment with antibiotics revealed decreases in the classic anti-inflammatory commensals such as Lactobacillus and increases in E. coli after treatment, which should caution the use of antimicrobials for “Eradication” of uropathogens, particularly in asymptomatic patients.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Gottschick C, Deng ZL, Vital M, Masur C, Abels C, Pieper DH, et al. The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment. Microbiome. 2017;5(1):99. https://doi.org/10.1186/s40168-017-0305-3.

    Article  PubMed  PubMed Central  Google Scholar 

  81. Modena BD, Milam R, Harrison F, Cheeseman JA, Abecassis MM, Friedewald JJ, et al. Changes in urinary microbiome populations correlate in kidney transplants with interstitial fibrosis and tubular atrophy documented in early surveillance biopsies. Am J Transplant Off J Am Soc Transplant Am Soc Transplant Surg. 2017;17(3):712–23. https://doi.org/10.1111/ajt.14038.

    Article  CAS  Google Scholar 

  82. Bucevic Popovic V, Situm M, Chow CT, Chan LS, Roje B, Terzic J. The urinary microbiome associated with bladder cancer. Sci Rep. 2018;8(1):12157. https://doi.org/10.1038/s41598-018-29054-w.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, et al. Profiling the urinary microbiota in male patients with bladder cancer in China. Front Cell Infect Microbiol. 2018;8:167. https://doi.org/10.3389/fcimb.2018.00167.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Viljoen KS, Dakshinamurthy A, Goldberg P, Blackburn JM. Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer. PLoS One. 2015;10(3):e0119462. https://doi.org/10.1371/journal.pone.0119462.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Bullman S, Pedamallu CS, Sicinska E, Clancy TE, Zhang X, Cai D, et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science. 2017;358(6369):1443–8. https://doi.org/10.1126/science.aal5240.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Raoult D. Is there a link between urinary microbiota and bladder cancer? Eur J Epidemiol. 2017;32(3):255. https://doi.org/10.1007/s10654-016-0213-z.

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Lee JA, Stern JM. Understanding the link between gut microbiome and urinary stone disease. Curr Urol Rep. 2019;20(5):19. https://doi.org/10.1007/s11934-019-0882-8.

    Article  PubMed  Google Scholar 

  89. Tang R, Jiang Y, Tan A, Ye J, Xian X, Xie Y, et al. 16S rRNA gene sequencing reveals altered composition of gut microbiota in individuals with kidney stones. Urolithiasis. 2018;46(6):503–14. https://doi.org/10.1007/s00240-018-1037-y.

    Article  CAS  PubMed  Google Scholar 

  90. Stern JM, Moazami S, Qiu Y, Kurland I, Chen Z, Agalliu I, et al. Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers. Urolithiasis. 2016;44(5):399–407. https://doi.org/10.1007/s00240-016-0882-9.

    Article  PubMed  Google Scholar 

  91. Suryavanshi MV, Bhute SS, Jadhav SD, Bhatia MS, Gune RP, Shouche YS. Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures. Sci Rep. 2016;6:34712. https://doi.org/10.1038/srep34712.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Ticinesi A, Milani C, Guerra A, Allegri F, Lauretani F, Nouvenne A, et al. Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers. Gut. 2018;67(12):2097–106. https://doi.org/10.1136/gutjnl-2017-315734.

    Article  CAS  PubMed  Google Scholar 

  93. Dornbier RA, Bajic P, Van Kuiken M, Jardaneh A, Lin H, Gao X, et al. The microbiome of calcium-based urinary stones. Urolithiasis. 2019. https://doi.org/10.1007/s00240-019-01146-w.

  94. Amimanan P, Tavichakorntrakool R, Fong-Ngern K, Sribenjalux P, Lulitanond A, Prasongwatana V, et al. Elongation factor Tu on Escherichia coli isolated from urine of kidney stone patients promotes calcium oxalate crystal growth and aggregation. Sci Rep. 2017;7(1):2953. https://doi.org/10.1038/s41598-017-03213-x.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Barr-Beare E, Saxena V, Hilt EE, Thomas-White K, Schober M, Li B, et al. The interaction between Enterobacteriaceae and calcium oxalate deposits. PLoS One. 2015;10(10):e0139575. https://doi.org/10.1371/journal.pone.0139575.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Chutipongtanate S, Sutthimethakorn S, Chiangjong W, Thongboonkerd V. Bacteria can promote calcium oxalate crystal growth and aggregation. J Biol Inorg Chem. 2013;18(3):299–308. https://doi.org/10.1007/s00775-012-0974-0.

    Article  CAS  PubMed  Google Scholar 

  97. Schwaderer AL, Wolfe AJ. The association between bacteria and urinary stones. Annals of translational medicine. 2017;5(2):32. https://doi.org/10.21037/atm.2016.11.73.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. De Ferrari ME, Macaluso M, Brunati C, Pozzoli R, Colussi G. Hypocitraturia and Ureaplasma urealyticum urinary tract infection in patients with idiopathic calcium nephrolithiasis. Nephrol Dial Transplant. 1996;11(6):1185. https://doi.org/10.1093/oxfordjournals.ndt.a027486.

    Article  PubMed  Google Scholar 

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A. Lenore Ackerman has no conflict of interest. Toby C. Chai has no conflict of interest.

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Ackerman, A.L., Chai, T.C. The Bladder is Not Sterile: an Update on the Urinary Microbiome. Curr Bladder Dysfunct Rep 14, 331–341 (2019). https://doi.org/10.1007/s11884-019-00543-6

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