nefrНефрологияNephrology (Saint-Petersburg)1561-62742541-9439Pavlov First Saint-Petersburg State Medical University10.36485/1561-6274-2022-26-3-52-58nefr-2138Research ArticleОБЗОРЫ И ЛЕКЦИИREVIEWS AND LECTURESБактерии и вирусы в моче в норме и при патологии (уробиом и уровиром)Bacteria and viruses in urine in normal and pathology (urobiome and urovirome)https://orcid.org/0000-0003-2054-3419КуприенкоН. Б.KuprienkoN. B.

Наталья Борисовна Куприенко, доц., канд. мед. наук

197022

ул. Льва Толстого, д. 6–8

Санкт-Петербург

тел.: (812) 338-7166

Natalya B. Kuprienko, Associate professor, MD, PhD

Department of pediatrics

197022

Lev Tolstoу str., 6-8

Saint Petersburg

Phone: 8(812) 338-7166

n-b-k@bk.ruhttps://orcid.org/0000-0002-0581-7285СмирноваН. Н.SmirnovaN. N.

Наталия Николаевна Смирнова, проф., д-р мед. наук

197022

ул. Льва Толстого, д. 6–8

Санкт-Петербург

Тел.: (812) 338-7166

Natalia N. Smirnova, Professor, MD, PhD, DMedSci

Department of pediatrics

197022

Lev Tolstoу str., 6-8

Saint Petersburg

Phone: 8(812) 338-7166

nephro-uro-kids@mail.ruПервый Санкт-Петербургский государственный медицинский университет им. акад. И. П. ПавловаРоссияPavlov First Saint Petersburg State Medical UniversityRussian Federation2022100920222635258Copyright © Куприенко Н.Б., Смирнова Н.Н., 20222022Куприенко Н.Б., Смирнова Н.Н.Kuprienko N.B., Smirnova N.N.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://journal.nephrolog.ru/jour/article/view/2138

   Термин «микробиота» относится к группе бактерий, а также вирусов, простейших, грибов и архей, связанных со специфической нишей макроорганизма. В последние годы усилился интерес к вирусному компоненту микробиоты – вирому. Лучше всего изучен микробиом кишечника. Изучение микробиома и вирома мочи и органов мочевой системы только началось. В обзоре представлены данные об эукариотических вирусах и бактериофагах в органах мочевой системы в физиологических и патологических условиях. В перспективе исследование уробиома и уровирома позволит пересмотреть подходы к терапии нефроурологической патологии.

   The term "microbiota" refers to a group of bacteria, as well as viruses, protozoa, fungi, and archaea associated with a specific niche of macroorganism. In recent years, interest in the viral component of the microbiota, virome, has increased. The gut microbiome is best studied. The study of the microbiome and urine virome and urinary organs has just begun. The review presents data on eukaryotic viruses and bacteriophages in the urinary system organs under physiological and pathological conditions. In the future, the study of urobiome and urovirome will allow revising approaches to therapy of nephro-urological pathology.

уробиомуровиромбиофагимикробиом мочевой системымикробиотаurobiomeuroviromebiofagesurinary tract microbiomemicrobiotaReferencesCho I., Blaser M. J. The human microbiome: At the interface of health and disease. Nat Rev Genet 2012;13:260–270. doi: 10.1038/nrg3182Cho I., Blaser M. J. The human microbiome: At the interface of health and disease. Nat Rev Genet 2012;13:260–270. doi: 10.1038/nrg3182Berg G., Rybakova D., Fischer D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 2020 Jun 30; 8 (1): 103. doi: 10.1186/s40168-020-00875-0Berg G., Rybakova D., Fischer D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 2020 Jun 30; 8 (1): 103. doi: 10.1186/s40168-020-00875-0Малаева Е. Г. Инфекции мочевыводящих путей и микробиота / Е. Г. Малаева // Проблемы здоровья и экологии. – 2021. – 18 (3): 5–14. doi: https://doi.org/10.51523/2708-6011.2021-18-3-1 / Malaeva E. G. Urinary tract infections and microbiota. Health and Ecology Issues 2021;18 (3): 5–14. (In Russ.) doi: https://doi.org/10.51523/2708-6011.2021-18-3-1Малаева Е. Г. Инфекции мочевыводящих путей и микробиота / Е. Г. Малаева // Проблемы здоровья и экологии. – 2021. – 18 (3): 5–14. doi: https://doi.org/10.51523/2708-6011.2021-18-3-1 / Malaeva E. G. Urinary tract infections and microbiota. Health and Ecology Issues 2021;18 (3): 5–14. (In Russ.) doi: https://doi.org/10.51523/2708-6011.2021-18-3-1Gilbert 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 Apr 10; 24 (4): 392–400. doi: 10.1038/nm.4517Gilbert 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 Apr 10; 24 (4): 392–400. doi: 10.1038/nm.4517Ackerman A. L., Chai T. C. The Bladder is Not Sterile: An Update on the Urinary Microbiome. Curr Bladder Dysfunct Rep 2019; 14: 331–341. doi: 10.1007/s11884-019-00543-6Ackerman A. L., Chai T. C. The Bladder is Not Sterile: An Update on the Urinary Microbiome. Curr Bladder Dysfunct Rep 2019; 14: 331–341. doi: 10.1007/s11884-019-00543-6Breitbart M., Salamon P., Andresen B. et al. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 2002 Oct 29; 99 (22): 14250–14255. doi: 10.1073/pnas.202488399Breitbart M., Salamon P., Andresen B. et al. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 2002 Oct 29; 99 (22): 14250–14255. doi: 10.1073/pnas.202488399Santiago-Rodriguez T. M., Hollister E. B. Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut. Viruses 2019; 11: 656. doi: 10.3390/v11070656Santiago-Rodriguez T. M., Hollister E. B. Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut. Viruses 2019; 11: 656. doi: 10.3390/v11070656Zárate S., Taboada B., Yocupicio-Monroy M., Arias C. F. Human virome. Arch Med Res 2017; 48: 701–716. doi: 10.1016/j.arcmed.2018.01.005Zárate S., Taboada B., Yocupicio-Monroy M., Arias C. F. Human virome. Arch Med Res 2017; 48: 701–716. doi: 10.1016/j.arcmed.2018.01.005Santiago-Rodriguez T. M., Hollister E. B. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86: e01794-20. doi: 10.1128/AEM.01794-20Santiago-Rodriguez T. M., Hollister E. B. Potential Applications of Human Viral Metagenomics and Reference Materials: Considerations for Current and Future Viruses. Appl Environ Microbiol 2020; 86: e01794-20. doi: 10.1128/AEM.01794-20Liang G., Bushman F. D. The human virome: Assembly, composition and host interactions. Nat Rev Microbiol 2021; 19: 514–527. doi: 10.1038/s41579-021-00536-5Liang G., Bushman F. D. The human virome: Assembly, composition and host interactions. Nat Rev Microbiol 2021; 19: 514–527. doi: 10.1038/s41579-021-00536-5Fulci V., Stronati L., Cucchiara S., Laudadio I., Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22: 4127. doi: 10.3390/ijms22084127Fulci V., Stronati L., Cucchiara S., Laudadio I., Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22: 4127. doi: 10.3390/ijms22084127Koonin E. V., Dolja V. V., Krupovic M. The healthy human virome: From virus–host symbiosis to disease. Curr Opin Virol 2021; 47: 86–94. doi: 10.1016/j.coviro.2021.02.002Koonin E. V., Dolja V. V., Krupovic M. The healthy human virome: From virus–host symbiosis to disease. Curr Opin Virol 2021; 47: 86–94. doi: 10.1016/j.coviro.2021.02.002Zaczek M., Weber-Dabrowska B., Miedzybrodzki R., Górski A. Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications. Microorganisms 2020; 8: 1802. doi: 10.3390/microorganisms8111802Zaczek M., Weber-Dabrowska B., Miedzybrodzki R., Górski A. Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications. Microorganisms 2020; 8: 1802. doi: 10.3390/microorganisms8111802Giulia Freer, Fabrizio Maggi, Mauro Pistello Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. Curr Med Chem 2019; 26 (6): 1027–1044. doi: 10.2174/0929867324666171005112921Giulia Freer, Fabrizio Maggi, Mauro Pistello Virome and Inflammasomes, a Finely Tuned Balance with Important Consequences for the Host Health. Curr Med Chem 2019; 26 (6): 1027–1044. doi: 10.2174/0929867324666171005112921Divers J., Langefeld C. D., Lyles D. S., Ma L., Freedman B. I. Protective association between JC polyoma viruria and kidney disease. Curr Opin Nephrol Hypertens 2019; 28: 65–69. doi: 10.1097/MNH.0000000000000464Divers J., Langefeld C. D., Lyles D. S., Ma L., Freedman B. I. Protective association between JC polyoma viruria and kidney disease. Curr Opin Nephrol Hypertens 2019; 28: 65–69. doi: 10.1097/MNH.0000000000000464Navarro F., Muniesa M. Phages in the Human Body. Front Microbiol 2017;8:566. doi: 10.3389/fmicb.2017.00566Navarro F., Muniesa M. Phages in the Human Body. Front Microbiol 2017;8:566. doi: 10.3389/fmicb.2017.00566Garretto A., Thomas-White K., Wolfe A. J., Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virol 2018; 99: 1141–1146. doi: 10.1099/jgv.0.001097Garretto A., Thomas-White K., Wolfe A. J., Putonti C. Detecting viral genomes in the female urinary microbiome. J Gen Virol 2018; 99: 1141–1146. doi: 10.1099/jgv.0.001097Zaczek M., Weber-Dabrowska B., Miedzybrodzki R., Gоrski A. Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications. Microorganisms 2020; 8: 1802. doi: 10.3390/microorganisms8111802Zaczek M., Weber-Dabrowska B., Miedzybrodzki R., Gоrski A. Phage Prevalence in the Human Urinary Tract-Current Knowledge and Therapeutic Implications. Microorganisms 2020; 8: 1802. doi: 10.3390/microorganisms8111802Van Belleghem J. D., Dabrowska K., Vaneechoutte M., Barr J. J., Bollyky P. L. Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System. Viruses 2018; 11: 10. doi: 10.3390/v11010010Van Belleghem J. D., Dabrowska K., Vaneechoutte M., Barr J. J., Bollyky P. L. Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System. Viruses 2018; 11: 10. doi: 10.3390/v11010010Salabura A., Łuniewski A., Kucharska M. et al. Urinary Tract Virome as an Urgent Target for Metagenomics. Life 2021; 11: 1264. https://doi.org/10.3390/life11111264Salabura A., Łuniewski A., Kucharska M. et al. Urinary Tract Virome as an Urgent Target for Metagenomics. Life 2021; 11: 1264. https://doi.org/10.3390/life11111264Garretto A., Hatzopoulos T., Putonti C. virMine: Automated detection of viral sequences from complex metagenomic samples. PeerJ 2019; 7: e6695. doi: 10.7717/peerj.6695Garretto A., Hatzopoulos T., Putonti C. virMine: Automated detection of viral sequences from complex metagenomic samples. PeerJ 2019; 7: e6695. doi: 10.7717/peerj.6695Aragón I. M., Herrera-Imbroda B., Queipo-Ortuño M. I. et al. The Urinary Tract Microbiome in Health and Disease. Eur Urol Focus 2018; 4: 128–138. doi: 10.1016/j.euf.2016.11.001Aragón I. M., Herrera-Imbroda B., Queipo-Ortuño M. I. et al. The Urinary Tract Microbiome in Health and Disease. Eur Urol Focus 2018; 4: 128–138. doi: 10.1016/j.euf.2016.11.001Magistro G., Stief C. G. The Urinary Tract Microbiome: The Answer to All Our Open Questions? Eur Urol Focus 2019; 5: 36–38Magistro G., Stief C. G. The Urinary Tract Microbiome: The Answer to All Our Open Questions? Eur Urol Focus 2019; 5: 36–38Четвериков А. В. Микробиом мочи и его влияние на стабильность коллоидных свойств у больных уролитиазом / А. В. Четвериков, Е. Т. Голощапов, Е. С. Белозеров // Ульяновский медико-биологический журнал. – 2019. – 4: 12–23 / Chetverikov A. V., Goloshchapov E. T., Belozerov E. S. Urine microbiome and its effect on the stability of colloidal properties in patients with urolithiasis. Uljanov medico-biological J 2019; 4: 12–23 (In Russ.)Четвериков А. В. Микробиом мочи и его влияние на стабильность коллоидных свойств у больных уролитиазом / А. В. Четвериков, Е. Т. Голощапов, Е. С. Белозеров // Ульяновский медико-биологический журнал. – 2019. – 4: 12–23 / Chetverikov A. V., Goloshchapov E. T., Belozerov E. S. Urine microbiome and its effect on the stability of colloidal properties in patients with urolithiasis. Uljanov medico-biological J 2019; 4: 12–23 (In Russ.)Gerber D., Forster C. S., Hsieh M. The Role of the Genitourinary Microbiome in Pediatric Urology: A Review. Curr Urol Rep 2018; 19: 13. doi: 10.1007/s11934-018-0763-6Gerber D., Forster C. S., Hsieh M. The Role of the Genitourinary Microbiome in Pediatric Urology: A Review. Curr Urol Rep 2018; 19: 13. doi: 10.1007/s11934-018-0763-6Xu R., Deebel N., Casals R., Dutta R., Mirzazadeh M. A new gold rush: A review of current and developing diagnostic tools for urinary tract infections. Diagnostics 2021; 11: 479. doi: 10.3390/diagnostics11030479Xu R., Deebel N., Casals R., Dutta R., Mirzazadeh M. A new gold rush: A review of current and developing diagnostic tools for urinary tract infections. Diagnostics 2021; 11: 479. doi: 10.3390/diagnostics11030479Pohl H. G., Groah S. L., Pérez-Losada M. The urine microbiome of healthy men and women differs by urine collection method. Int Neurourol J 2020; 24: 41–51. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136448/Pohl H. G., Groah S. L., Pérez-Losada M. The urine microbiome of healthy men and women differs by urine collection method. Int Neurourol J 2020; 24: 41–51. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7136448/Brubaker L., Gourdine J.-P. F., Siddiqui N. Y. et al. Forming consensus to advance urobiome research. Msystems 2021; 6: e01371-20. doi: 10.1128/mSystems.01371-20Brubaker L., Gourdine J.-P. F., Siddiqui N. Y. et al. Forming consensus to advance urobiome research. Msystems 2021; 6: e01371-20. doi: 10.1128/mSystems.01371-20Herreros M. L., Gili P., del Valle R., Barrios A., Pacheco M., Sánchez A. Urine collection methods for infants under 3 months of age in clinical practice. Pediatr Nephrol 2020; 36; 3899–3904. doi: 10.1007/s00467-021-05142-4Herreros M. L., Gili P., del Valle R., Barrios A., Pacheco M., Sánchez A. Urine collection methods for infants under 3 months of age in clinical practice. Pediatr Nephrol 2020; 36; 3899–3904. doi: 10.1007/s00467-021-05142-4Perez-Carrasco V., Soriano-Lerma A., Soriano M., Gutiérrez-Fernández J., Garcia-Salcedo J. A. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front Cell Infect Microbiol 2021; 11: 421. doi: 10.3389/fcimb.2021.617002Perez-Carrasco V., Soriano-Lerma A., Soriano M., Gutiérrez-Fernández J., Garcia-Salcedo J. A. Urinary Microbiome: Yin and Yang of the Urinary Tract. Front Cell Infect Microbiol 2021; 11: 421. doi: 10.3389/fcimb.2021.617002Kieft K., Zhou Z., Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 2020 Jun 10; 8 (1): 90. doi: 10.1186/s40168-020-00867-0Kieft K., Zhou Z., Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 2020 Jun 10; 8 (1): 90. doi: 10.1186/s40168-020-00867-0Santiago-Rodriguez T. M., Ly M., Bonilla N., Pride D. T. The human urine virome in association with urinary tract infections. Front Microbiol 2015 Jan 23; 6: 14. doi: 10.3389/fmicb.2015.00014Santiago-Rodriguez T. M., Ly M., Bonilla N., Pride D. T. The human urine virome in association with urinary tract infections. Front Microbiol 2015 Jan 23; 6: 14. doi: 10.3389/fmicb.2015.00014Stern J., Miller G., Li X., Saxena D. Virome and bacteriome: Two sides of the same coin. Curr Opin Virol 2019; 37: 37–43. doi: 10.1016/j.coviro.2019.05.007Stern J., Miller G., Li X., Saxena D. Virome and bacteriome: Two sides of the same coin. Curr Opin Virol 2019; 37: 37–43. doi: 10.1016/j.coviro.2019.05.007Neil J. A, Cadwell K. The Intestinal Virome and Immunity. J Immunol 2018; 201: 1615–1624. doi: 10.4049/jimmunol.1800631Neil J. A, Cadwell K. The Intestinal Virome and Immunity. J Immunol 2018; 201: 1615–1624. doi: 10.4049/jimmunol.1800631Sigdel T. K., Mercer N., Nandoe S., Nicora C. D., Burnum-Johnson K., Qian W. J., Sarwal M. M. Urinary Virome Per-turbations in Kidney Transplantation. Front Med 2019; 5: 72. doi: 10.3389/fmed.2018.00072Sigdel T. K., Mercer N., Nandoe S., Nicora C. D., Burnum-Johnson K., Qian W. J., Sarwal M. M. Urinary Virome Per-turbations in Kidney Transplantation. Front Med 2019; 5: 72. doi: 10.3389/fmed.2018.00072Kinneman L., Zhu W., Wong W. S. W. et al. Assessment of the urinary microbiome in children younger than 48 months. Pediatr. Infect Dis J 2020; 39: 565–570. doi: 10.1097/INF.0000000000002622Kinneman L., Zhu W., Wong W. S. W. et al. Assessment of the urinary microbiome in children younger than 48 months. Pediatr. Infect Dis J 2020; 39: 565–570. doi: 10.1097/INF.0000000000002622Robertson R. C., Manges A. R., Finlay B. B., Prendergast A. J. The Human Microbiome and Child Growth—First 1000 Days and Beyond. Trends Microbiol 2019; 27: 131–147. doi: 10.1016/j.tim.2018.09.008Robertson R. C., Manges A. R., Finlay B. B., Prendergast A. J. The Human Microbiome and Child Growth—First 1000 Days and Beyond. Trends Microbiol 2019; 27: 131–147. doi: 10.1016/j.tim.2018.09.008Fredsgaard L., Thorsteinsson K., Bundgaard-Nielsen C., Ammitzbøll N., Leutscher P., Chai Q., Jensen A. M., Sørensen S., Pedersen L. M., Hagstrøm S. et al. Description of the voided urinary microbiota in asymptomatic prepubertal children—A pilot study. J Pediatr Urol 2021; 17: 545.e1–545.e8. doi: 10.1016/j.jpurol.2021.03.019Fredsgaard L., Thorsteinsson K., Bundgaard-Nielsen C., Ammitzbøll N., Leutscher P., Chai Q., Jensen A. M., Sørensen S., Pedersen L. M., Hagstrøm S. et al. Description of the voided urinary microbiota in asymptomatic prepubertal children—A pilot study. J Pediatr Urol 2021; 17: 545.e1–545.e8. doi: 10.1016/j.jpurol.2021.03.019Kassiri B., Shrestha E., Kasprenski M., Antonescu C., Florea L. D., Sfanos K. S., Wang M. H. A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males. Urology 2019; 131: 204–210. doi: 10.1016/j.urology.2019.05.031Kassiri B., Shrestha E., Kasprenski M., Antonescu C., Florea L. D., Sfanos K. S., Wang M. H. A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males. Urology 2019; 131: 204–210. doi: 10.1016/j.urology.2019.05.031Gerber D., Forster C. S., Hsieh M. The Role of the Genitourinary Microbiome in Pediatric Urology: A Review. Curr Urol Rep 2018; 19: 13. doi: 10.1007/s11934-018-0763-6Gerber D., Forster C. S., Hsieh M. The Role of the Genitourinary Microbiome in Pediatric Urology: A Review. Curr Urol Rep 2018; 19: 13. doi: 10.1007/s11934-018-0763-6Lee K. W., Song H. Y., Kim Y. H. The microbiome in urological diseases. Investig Clin Urol 2020; 61: 338–348. doi: 10.4111/icu.2020.61.4.338Lee K. W., Song H. Y., Kim Y. H. The microbiome in urological diseases. Investig Clin Urol 2020; 61: 338–348. doi: 10.4111/icu.2020.61.4.338Guanxiang Liang, Chunyu Zhao , Huanjia Zhang Lisa Mattei et al. The stepwise assembly of the neonatal virome is modulated by breastfeeding Nature 2020 May; 581 (7809): 470–474. doi: 10.1038/s41586-020-2192-1Guanxiang Liang, Chunyu Zhao , Huanjia Zhang Lisa Mattei et al. The stepwise assembly of the neonatal virome is modulated by breastfeeding Nature 2020 May; 581 (7809): 470–474. doi: 10.1038/s41586-020-2192-1Blanca Taboada, Patricia Morán, Angélica Serrano-Vázquez, Pavel Iša, Liliana Rojas-Velázquez, Horacio Pérez-Juárez, Susana López, Javier Torres, Cecilia Ximenez, Carlos F. Arias The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021 Apr 14; 16 (4): e0240958. doi: 10.1371/journal.pone.0240958Blanca Taboada, Patricia Morán, Angélica Serrano-Vázquez, Pavel Iša, Liliana Rojas-Velázquez, Horacio Pérez-Juárez, Susana López, Javier Torres, Cecilia Ximenez, Carlos F. Arias The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021 Apr 14; 16 (4): e0240958. doi: 10.1371/journal.pone.0240958

The authors declare that there are no conflicts of interest present.