Original Research ARTICLE

Front. Cell. Infect. Microbiol., 15 August 2013 | doi: 10.3389/fcimb.2013.00041

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults

Debbie A. Lewis1,2, Richard Brown3, Jon Williams4, Paul White1, S. Kim Jacobson4,5, Julian R. Marchesi3* and Marcus J. Drake2,6*
  • 1Department of Engineering Design and Mathematics, University of the West of England, Bristol, UK
  • 2Bristol Urological Institute, Southmead Hospital, Bristol, UK
  • 3School of Biosciences, Cardiff University, Cardiff, UK
  • 4North Bristol NHS Trust, Southmead Hospital, Bristol, UK
  • 5Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
  • 6School of Clinical Sciences, University of Bristol, Bristol, UK

The urinary microbiome of healthy individuals and the way it alters with ageing have not been characterized and may influence disease processes. Conventional microbiological methods have limited scope to capture the full spectrum of urinary bacterial species. We studied the urinary microbiota from a population of healthy individuals, ranging from 26 to 90 years of age, by amplification of the 16S rRNA gene, with resulting amplicons analyzed by 454 pyrosequencing. Mid-stream urine (MSU) was collected by the “clean-catch” method. Quantitative PCR of 16S rRNA genes in urine samples, allowed relative enumeration of the bacterial loads. Analysis of the samples indicates that females had a more heterogeneous mix of bacterial genera compared to the male samples and generally had representative members of the phyla Actinobacteria and Bacteroidetes. Analysis of the data leads us to conclude that a “core” urinary microbiome could potentially exist, when samples are grouped by age with fluctuation in abundance between age groups. The study also revealed age-specific genera Jonquetella, Parvimonas, Proteiniphilum, and Saccharofermentans. In conclusion, conventional microbiological methods are inadequate to fully identify around two-thirds of the bacteria identified in this study. Whilst this proof-of-principle study has limitations due to the sample size, the discoveries evident in this sample data are strongly suggestive that a larger study on the urinary microbiome should be encouraged and that the identification of specific genera at particular ages may be relevant to pathogenesis of clinical conditions.

Keywords: bladder microbiome, pyrosequencing, urinary microbiome, bladder disease, microbiological methods

Citation: Lewis DA, Brown R, Williams J, White P, Jacobson SK, Marchesi JR and Drake MJ (2013) The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front. Cell. Infect. Microbiol. 3:41. doi: 10.3389/fcimb.2013.00041

Received: 24 February 2013; Accepted: 25 July 2013;
Published online: 15 August 2013.

Edited by:

Alain Stintzi, Ottawa Institute of Systems Biology, Canada

Reviewed by:

David Nelson, Indiana University Bloomington, USA
Valerio Iebba, ‘Sapienza’ University of Rome, Italy

Copyright © 2013 Lewis, Brown, Williams, White, Jacobson, Marchesi and Drake. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Julian R. Marchesi, School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK e-mail: marchesijr@cardiff.ac.uk;
Marcus J. Drake, Bristol Urological Institute, Southmead Hospital, Bristol BS10 5NB, UK e-mail: marcus.drake@bui.ac.uk

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