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The human urobiome

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Abstract

Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.

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Acknowledgements

We would like to thank the members of the Loyola Urinary Education and Research Collaborative for their contributions to the work described.

Funding

The authors gratefully acknowledge the following funding: AJW and LB by NIH Grant R01 DK104718, QD by NIH Grant 5R01AI116706 (subcontracted from Indiana University School of Medicine, PI, David Nelson), and CP by NSF Grant 1661357. No funding, supplies, or services were received from any commercial organization.

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Authors and Affiliations

  1. Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA

    L. Brubaker

  2. Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA

    C. Putonti

  3. Department of Biology, Loyola University Chicago, Chicago, IL, USA

    C. Putonti

  4. Department of Medicine and Center for Biomedical Informatics, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA

    Q. Dong

  5. Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60089, USA

    A. J. Wolfe

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  1. L. Brubaker
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  2. C. Putonti
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  3. Q. Dong
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  4. A. J. Wolfe
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LB, CP, QD and AJW wrote and edited the manuscript.

Corresponding author

Correspondence to A. J. Wolfe.

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Conflict of interest

Dr. Wolfe discloses research support from the NIH, the DOD, Astellas Scientific and Medical Affairs and Kimberly Clark Corporation. He also discloses membership on the advisory board for Urobiome Therapeutics. Dr. Brubaker discloses research funding from NIH and editorial stipends from Female Pelvic Medicine & Reconstructive Surgery, UpToDate and JAMA. The remaining authors report no disclosures.

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Brubaker, L., Putonti, C., Dong, Q. et al. The human urobiome. Mamm Genome 32, 232–238 (2021). https://doi.org/10.1007/s00335-021-09862-8

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