1. Structure , function and diversity of the healthy human microbiome. Nature [Internet]. 2012;486:207–14. Available from: http://dx.doi.org/10.1038/nature11234
2. 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;(11):1–12.
3. 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.
4. Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, et al. The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. PLoS One. 2011;6(5):1–5.
5. Nelson DE, van der Pol B, Dong Q, Revanna K V., Fan B, Easwaran S, et al. Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. PLoS One. 2010;5(11):1–7.
6. 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.
7. Thomas-White K, Forster SC, Kumar N, Kuiken M Van, Putonti C, Stares MD, et al. Culturing of female bladder bacteria reveals an interconnected urogenital microbiota. Nat Commun [Internet]. 2018;(9):1557. Available from: http://dx.doi.org/10.1038/s41467-018-03968-5
8. Hourigan SK, Zhu W, Wong WSW, Clemency NC, Provenzano M, Vilboux T, et al. Studying the urine microbiome in superficial bladder cancer : samples obtained by midstream voiding versus cystoscopy. BMC Urol. 2020;20(5):1–8.
9. Pohl HG, Groah SL, Pérez-losada M, Ljungberg I, Sprague BM, Chandal N, et al. The Urine Microbiome of Healthy Men and Women Differs by Urine Collection Method. Int Neurourol J. 2020;24(1):41–51.
10. Bajic P, Kuiken ME van, Burge BK, Kirshenbaum EJ, Joyce CJ, Wolfe AJ, et al. Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms. Eur Urol Focus [Internet]. 2020;15(6):376–82. Available from: https://doi.org/10.1016/j.euf.2018.08.001
11. Thomas-White KJ, Hilt EE, Fok C. Incontinence Medication Response Relates to the Female Urinary Microbiota. Int Urogynecol J. 2016;27(5):723–33.
12. 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 [Internet]. 2018;50(6):1123–30. Available from: https://doi.org/10.1007/s11255-018-1860-7
13. Fouts D, Pieper R, Szpakowski S. 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. 2012;10(174).
14. 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.
15. Pederzoli F, Ferrarese R, Amato V, Locatelli I, Alchera E, Luciano R, et al. Sex-specific Alterations in the Urinary and Tissue Microbiome in Therapy-naïve Urothelial Bladder Cancer Patients. Eur Urol Oncol. 2020;3(6):784–8.
16. Shoskes DA, Wang H, Polackwich AS, Tucky B, Altemus J, Eng C. Analysis of Gut Microbiome Reveals Significant Differences between Men with Chronic Prostatitis / Chronic Pelvic Pain Syndrome and Controls. J Urol [Internet]. 2016;196(2):435–41. Available from: http://dx.doi.org/10.1016/j.juro.2016.02.2959
17. Siddiqui H, Lagesen K, Nederbragt AJ, Jeansson SL, Jakobsen KS. Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiol [Internet]. 2012;12:205. Available from: http://www.biomedcentral.com/1471-2180/12/205
18. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 2011 Mar;108 Suppl(Suppl 1):4516–22.
19. Vetrovsky T, Baldrian P, Morais D. SEED 2: a user-friendly platfomr for amplicon high-throughput sequencing data analyses. Bioinformatics. 2018;34(13):2292–4.
20. Aronesty E. Comparison of Sequencing Utility Programs. Open Bioinforma J. 2013;7(1):1–8.
21. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013 Oct;10(10):996–8.
22. Větrovský T, Baldrian P. Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biol Fertil Soils [Internet]. 2013;49(8):1027–37. Available from: https://doi.org/10.1007/s00374-013-0801-y
23. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: Data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(D1):633–42.
24. Oksanen AJ, Blanchet FG, Friendly M, Kindt R, Legendre P, Mcglinn D, et al. Package ‘ vegan .’ Community Ecol Packag. 2017;5(December 2018).
25. McMurdie PJ, Holmes S. Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS One. 2013;8(4).
26. Roesch LFW, Dobbler PT, Pylro VS, Kolaczkowski B, Drew JC, Triplett EW. pime: A package for discovery of novel differences among microbial communities. Mol Ecol Resour. 2020 Mar;20(2):415–28.
27. Ihaka R, Gentleman R. R: A Language for Data Analysis and Graphics. J Comput Graph Stat [Internet]. 1996;5(3):299–314. Available from: https://www.tandfonline.com/doi/abs/10.1080/10618600.1996.10474713
28. Chao A, Chazdon RL, Colwell RK, Shen T-J. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol Lett [Internet]. 2005;8(2):148–59. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1461-0248.2004.00707.x
29. Stevens BR, Roesch L, Thiago P, Russell JT, Pepine CJ, Holbert RC, et al. Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome. Mol Psychiatry. 2020 Jan;
30. Thomas-White KJ, Kliethermes S, Rickey L. Evaluation of the Urinary Microbiota of Women With Uncomplicated Stress Urinary Incontinence. Am J Obs Gynecol. 2017;216(1).
31. Frolund M, Wikstrom A, Lidbrink P, Al-soud WA, Larsen N, Ahrens P. The bacterial microbiota in first-void urine from men with and without idiopathic urethritis. PLoS One. 2018;13(7):e0201380.
32. Popović VB, Šitum M, Chow CT, Chan LS. The urinary microbiome associated with bladder cancer. Sci Rep. 2018;8:12157.
33. Hafenbradl D, Keller M, Dirmeier R, Rachel R, Rossnagel P, Burggraf S, et al. Ferroglobus placidus gen. nov., sp. nov., A novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions. Arch Microbiol. 1996 Nov;166(5):308–14.
34. Wolfe AJ, Brubaker L. Urobiome updates: advances in urinary microbiome research. Nat Rev Urol. 2019;16(2):73–4.
35. 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 [Internet]. 2013;3(August):1–14. Available from: http://journal.frontiersin.org/article/10.3389/fcimb.2013.00041/abstract
36. Abelson B, Sun D, Que L, Nebel RA, Baker D, Popiel P, et al. Sex differences in lower urinary tract biology and physiology. Biol Sex Differ. 2018;9(1):1–13.
37. Price LB, Liu CM, Johnson KE, Aziz M, Lau MK, Bowers J, et al. The effects of circumcision on the penis microbiome. PLoS One. 2010;5(1):1–12.
38. Sathiananthamoorthy S, Malone-Lee J, Gill K, Tymon A, Nguyen TK, Gurung S, et al. Reassessment of Routine Midstream Culture in Diagnosis of Urinary Tract Infection. J Clin Microbiol. 2019;57(3):1–47.
39. 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).