Community profiling of the urinary microbiota: considerations for low-biomass samples

Lisa Karstens, Mark Asquith, Vincent Caruso, James T. Rosenbaum, Damien A. Fair, Jonathan Braun, W. Thomas Gregory, Rahel Nardos, Shannon K. McWeeney

Research output: Contribution to journalReview articlepeer-review

58 Scopus citations


Many studies have shown that the urinary tract harbours its own microbial community known as the urinary microbiota, which have been implicated in urinary tract disorders. This observation contradicts the long-held notion that urine is a sterile biofluid in the absence of acute infection of the urinary tract. In light of this new discovery, many basic questions that are crucial for understanding the role of the urinary microbiota in human health and disease remain unanswered. Given that the urinary microbiota is an emerging area of study, optimized techniques and protocols to identify microorganisms in the urinary tract are still being established. However, the low microbial biomass and close proximity to higher microbial biomass environments (for example, the vagina) present distinct methodological challenges for microbial community profiling of the urinary microbiota. A clear understanding of the unique technical considerations for obtaining and analysing low microbial biomass samples, as well the influence of key elements of experimental design and computational analysis on downstream interpretation, will improve our ability to interpret and compare results across methods and studies and is relevant for studies profiling the urinary microbiota and other sites of low microbial abundance.

Original languageEnglish (US)
Pages (from-to)735-749
Number of pages15
JournalNature Reviews Urology
Issue number12
StatePublished - Dec 1 2018
Externally publishedYes

Bibliographical note

Funding Information:
The authors thank R. Searles and L. Brubaker for helpful discussions. The authors also thank their funders who supported this work: L.K. is funded by the Oregon BIRCWH (Building Interdisciplinary Research Careers in Women’s Health) programme (US NIH award number K12HD043488), the NIH (award number (K01DK116706) and the Rheumatology Research Foundation. M.A. is funded by the Rheumatology Research Foundation and the Spondylitis Association of America. J.T.R. is funded by the NIH (award number R01EY029266), Research to Prevent Blindness (RPB), the Rheumatology Research Foundation, the Stan and Madelle Rosenfeld Family Trust, the William and Mary Bauman Family Foundation and the Spondylitis Association of America. J.B. is funded by the NIH (award numbers P01DK46763, P30CA016042 and UL1TR001881). D.A.F. is funded by the NIH (award numbers R01MH115357, R01MH105538, R01MH096773 and R00MH091238). S.K.M. is funded by the NIH (award numbers UL1TR002369 and U24TR002306). R.N. is funded by the Society of Urodynamics, Female Pelvic Medicine & Urogenital Reconstruction (Overactive Bladder Syndrome Urgency Urinary Incontinence grant). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or any other funding agency.

Publisher Copyright:
© 2018, Springer Nature Limited.


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