1887

Abstract

Viruses are the most abundant component of the human microbiota. Recent evidence has uncovered a rich diversity of viruses within the female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing of the bladder microbiome of 30 women: 10 asymptomatic ‘healthy’ women and 20 women with an overactive bladder. These metagenomes include sequences representative of human, bacterial and viral DNA. This analysis, however, focused specifically on viral sequences. Using the bioinformatic tool virMine, we discovered sequence fragments, as well as complete genomes, of bacteriophages and the eukaryotic virus JC polyomavirus. The method employed here is a critical proof of concept: the genomes of viral populations within the low-biomass bladder microbiota can be reconstructed through whole-genome sequencing of the entire microbial community.

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2018-06-11
2019-08-23
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References

  1. Price TK, Dune T, Hilt EE, Thomas-White KJ, Kliethermes S et al. The clinical urine culture: enhanced techniques improve detection of clinically relevant microorganisms. J Clin Microbiol 2016;54:1216–1222 [CrossRef][PubMed]
    [Google Scholar]
  2. Kass EH. Pyelonephritis and bacteriuria. A major problem in preventive medicine. Ann Intern Med 1962;56:46–53[PubMed]
    [Google Scholar]
  3. Wolfe AJ, Toh E, Shibata N, Rong R, Kenton K et al. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol 2012;50:1376–1383 [CrossRef][PubMed]
    [Google Scholar]
  4. Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoblach S et al. 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 [CrossRef][PubMed]
    [Google Scholar]
  5. Khasriya R, Sathiananthamoorthy S, Ismail S, Kelsey M, Wilson M et al. Spectrum of bacterial colonization associated with urothelial cells from patients with chronic lower urinary tract symptoms. J Clin Microbiol 2013;51:2054–2062 [CrossRef][PubMed]
    [Google Scholar]
  6. Hilt EE, McKinley K, Pearce MM, Rosenfeld AB, Zilliox MJ 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;52:871–876 [CrossRef][PubMed]
    [Google Scholar]
  7. Thomas-White KJ, Kliethermes S, Rickey L, Lukacz ES, Richter HE et al. Evaluation of the urinary microbiota of women with uncomplicated stress urinary incontinence. Am J Obstet Gynecol 2017;216:55.e1–55.e16 [CrossRef]
    [Google Scholar]
  8. Brubaker L, Nager CW, Richter HE, Visco A, Nygaard I et al. Urinary bacteria in adult women with urgency urinary incontinence. Int Urogynecol J 2014;25:1179–1184 [CrossRef][PubMed]
    [Google Scholar]
  9. Pearce MM, Zilliox MJ, Rosenfeld AB, Thomas-White KJ, Richter HE et al. The female urinary microbiome in urgency urinary incontinence. Am J Obstet Gynecol 2015;213:347.e1–347.e11 [CrossRef][PubMed]
    [Google Scholar]
  10. Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K et al. The female urinary microbiome: a comparison of women with and without urgency urinary incontinence. MBio 2014;5:e01283-14 [CrossRef][PubMed]
    [Google Scholar]
  11. Thomas-White KJ, Hilt EE, Fok C, Pearce MM, Mueller ER et al. Incontinence medication response relates to the female urinary microbiota. Int Urogynecol J 2016;27:723–733 [CrossRef]
    [Google Scholar]
  12. Nienhouse V, Gao X, Dong Q, Nelson DE, Toh E et al. Interplay between bladder microbiota and urinary antimicrobial peptides: mechanisms for human urinary tract infection risk and symptom severity. PLoS One 2014;9:e114185 [CrossRef][PubMed]
    [Google Scholar]
  13. Karstens L, Asquith M, Davin S, Stauffer P, Fair D et al. Does the urinary microbiome play a role in urgency urinary incontinence and its severity?. Front Cell Infect Microbiol 2016;6:78 [CrossRef][PubMed]
    [Google Scholar]
  14. Thomas-White KJ, Lin H, Gao X, Fok C, Mueller ER et al. Urinary symptoms and associated urinary microbes in urogynecologic surgical patients. 2018
  15. Thomas-White KJ, Gao X, Lin H, Fok C, Ghanayem K et al. Urinary microbes and post-operative urinary tract infection risk in urogynecologic surgical patients. 2018
  16. Iwasawa A, Kumamoto Y, Maruta H, Fukushima M, Tsukamoto T et al. Presence of human papillomavirus 6/11 DNA in condyloma acuminatum of the urinary bladder. Urol Int 1992;48:235–238 [CrossRef][PubMed]
    [Google Scholar]
  17. Echavarria M, Forman M, Ticehurst J, Dumler JS, Charache P. PCR method for detection of adenovirus in urine of healthy and human immunodeficiency virus-infected individuals. J Clin Microbiol 1998;36:3323–3326[PubMed]
    [Google Scholar]
  18. Karim RZ, Rose BR, Brammah S, Scolyer RA. Condylomata acuminata of the urinary bladder with HPV 11. Pathology 2005;37:176–178 [CrossRef][PubMed]
    [Google Scholar]
  19. Burián Z, Szabó H, Székely G, Gyurkovits K, Pankovics P et al. Detection and follow-up of torque teno midi virus ("small anelloviruses") in nasopharyngeal aspirates and three other human body fluids in children. Arch Virol 2011;156:1537–1541 [CrossRef][PubMed]
    [Google Scholar]
  20. Hirsch HH, Kardas P, Kranz D, Leboeuf C. The human JC polyomavirus (JCPyV): virological background and clinical implications. APMIS 2013;121:685–727 [CrossRef][PubMed]
    [Google Scholar]
  21. Rinaldo CH, Tylden GD, Sharma BN. The human polyomavirus BK (BKPyV): virological background and clinical implications. APMIS 2013;121:728–745 [CrossRef][PubMed]
    [Google Scholar]
  22. Assetta B, Atwood WJ. The biology of JC polyomavirus. Biol Chem 2017;398:839–855 [CrossRef][PubMed]
    [Google Scholar]
  23. Brown-Jaque M, Muniesa M, Navarro F. Bacteriophages in clinical samples can interfere with microbiological diagnostic tools. Sci Rep 2016;6:33000 [CrossRef][PubMed]
    [Google Scholar]
  24. Malki K, Sible E, Cooper A, Garretto A, Bruder K et al. Seven bacteriophages isolated from the female urinary microbiota. Genome Announc 2016;4:e01003-16 [CrossRef][PubMed]
    [Google Scholar]
  25. Miller-Ensminger T, Garretto A, Brenner J, Thomas-White K, Zambom A et al. Bacteriophages of the urinary microbiome. J Bacteriol 2018;200:e00738-17 [CrossRef][PubMed]
    [Google Scholar]
  26. Santiago-Rodriguez TM, Ly M, Bonilla N, Pride DT. The human urine virome in association with urinary tract infections. Front Microbiol 2015;6:14 [CrossRef][PubMed]
    [Google Scholar]
  27. Rani A, Ranjan R, McGee HS, Metwally A, Hajjiri Z et al. A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms. Sci Rep 2016;6:33327 [CrossRef][PubMed]
    [Google Scholar]
  28. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 2016;14:e1002533 [CrossRef][PubMed]
    [Google Scholar]
  29. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 2011;21:1616–1625 [CrossRef][PubMed]
    [Google Scholar]
  30. Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM et al. Healthy human gut phageome. Proc Natl Acad Sci USA 2016;113:10400–10405 [CrossRef][PubMed]
    [Google Scholar]
  31. Yilmaz S, Allgaier M, Hugenholtz P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 2010;7:943–944 [CrossRef][PubMed]
    [Google Scholar]
  32. Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun 2014;5:4498 [CrossRef][PubMed]
    [Google Scholar]
  33. Mokili JL, Dutilh BE, Lim YW, Schneider BS, Taylor T et al. Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness. PLoS One 2013;8:e58404 [CrossRef][PubMed]
    [Google Scholar]
  34. 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:e33865 [CrossRef][PubMed]
    [Google Scholar]
  35. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357–359 [CrossRef][PubMed]
    [Google Scholar]
  36. Joshi NA, Fass JN. 2011; Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. Available athttps://github.com/najoshi/sickle
  37. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  38. Garretto A, Hatzopoulos T, Kalesinskas L, Putonti C. 2017; virMine: Automated detection and annotation of complete viral genomes from complex metagenomic samples. Available athttps://github.com/thatzopoulos/virMine
  39. Krupovic M, Forterre P. Single-stranded DNA viruses employ a variety of mechanisms for integration into host genomes. Ann N Y Acad Sci 2015;1341:41–53 [CrossRef][PubMed]
    [Google Scholar]
  40. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011;39:W347–W352 [CrossRef][PubMed]
    [Google Scholar]
  41. Malki K, Shapiro JW, Price TK, Hilt EE, Thomas-White K et al. Genomes of Gardnerella strains reveal an abundance of prophages within the bladder microbiome. PLoS One 2016;11:e0166757 [CrossRef][PubMed]
    [Google Scholar]
  42. Koonin EV, Senkevich TG, Dolja VV. The ancient virus world and evolution of cells. Biol Direct 2006;1:29 [CrossRef][PubMed]
    [Google Scholar]
  43. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75 [CrossRef][PubMed]
    [Google Scholar]
  44. Teatero S, McGeer A, Li A, Gomes J, Seah C et al. Population structure and antimicrobial resistance of invasive serotype IV group B Streptococcus, Toronto, Ontario, Canada. Emerg Infect Dis 2015;21:585–591 [CrossRef][PubMed]
    [Google Scholar]
  45. Dieterle ME, Fina Martin J, Durán R, Nemirovsky SI, Sanchez Rivas C et al. Characterization of prophages containing "evolved" Dit/Tal modules in the genome of Lactobacillus casei BL23. Appl Microbiol Biotechnol 2016;100:9201–9215 [CrossRef][PubMed]
    [Google Scholar]
  46. Chang H, Wang M, Tsai RT, Lin HS, Huan JS et al. High incidence of JC viruria in JC-seropositive older individuals. J Neurovirol 2002;8:447–451 [CrossRef][PubMed]
    [Google Scholar]
  47. van Loy T, Thys K, Tritsmans L, Stuyver LJ. Quasispecies analysis of JC virus DNA present in urine of healthy subjects. PLoS One 2013;8:e70950 [CrossRef][PubMed]
    [Google Scholar]
  48. Khalili K, Gordon J, White MK. The polyomavirus, JCV and its involvement in human disease. Adv Exp Med Biol 2006;577:274–287 [CrossRef][PubMed]
    [Google Scholar]
  49. Shackelton LA, Rambaut A, Pybus OG, Holmes EC. JC virus evolution and its association with human populations. J Virol 2006;80:9928–9933 [CrossRef][PubMed]
    [Google Scholar]
  50. Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 2010;5:e9490 [CrossRef][PubMed]
    [Google Scholar]
  51. Agostini HT, Ryschkewitsch CF, Stoner GL. Genotype profile of human polyomavirus JC excreted in urine of immunocompetent individuals. J Clin Microbiol 1996;34:159–164[PubMed]
    [Google Scholar]
  52. Reid CE, Li H, Sur G, Carmillo P, Bushnell S et al. Sequencing and analysis of JC virus DNA from natalizumab-treated PML patients. J Infect Dis 2011;204:237–244 [CrossRef][PubMed]
    [Google Scholar]
  53. Saruwatari L, Sugimoto C, Kitamura T, Ohno N, Sakai E et al. Asian domains of four major genotypes of JC virus, Af2, B1-b, CY and SC. Arch Virol 2002;147:1–10 [CrossRef][PubMed]
    [Google Scholar]
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