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Research Article

Bacteriophages of the Urinary Microbiome

Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J. Wolfe, Catherine Putonti
Igor B. Zhulin, Editor
Taylor Miller-Ensminger
aBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
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Andrea Garretto
aBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
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Jonathon Brenner
bDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USA
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Krystal Thomas-White
cDepartment of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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Adriano Zambom
dDepartment of Mathematics and Statistics, Loyola University Chicago, Chicago, Illinois, USA
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Alan J. Wolfe
cDepartment of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
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Catherine Putonti
aBioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
bDepartment of Computer Science, Loyola University Chicago, Chicago, Illinois, USA
cDepartment of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
eDepartment of Biology, Loyola University Chicago, Chicago, Illinois, USA
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  • ORCID record for Catherine Putonti
Igor B. Zhulin
University of Tennessee at Knoxville
Roles: Editor
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DOI: 10.1128/JB.00738-17
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ABSTRACT

Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and human health have been discovered. In contrast to the gastrointestinal tract, the phages associated with the urinary microbiota are largely unknown. Preliminary metagenomic surveys of the urinary virome indicate a rich diversity of novel lytic phage sequences at an abundance far outnumbering that of eukaryotic viruses. These surveys, however, exclude the lysogenic phages residing within the bacteria of the bladder. To characterize this phage population, we examined 181 genomes representative of the phylogenetic diversity of bacterial species within the female urinary microbiota and found 457 phage sequences, 226 of which were predicted with high confidence. Phages were prevalent within the bladder bacteria: 86% of the genomes examined contained at least one phage sequence. Most of these phages are novel, exhibiting no discernible sequence homology to sequences in public data repositories. The presence of phages with substantial sequence similarity within the microbiota of different women supports the existence of a core community of phages within the bladder. Furthermore, the observed variation between the phage populations of women with and without overactive bladder symptoms suggests that phages may contribute to urinary health. To complement our bioinformatic analyses, viable phages were cultivated from the bacterial isolates for characterization; a novel coliphage was isolated, which is obligately lytic in the laboratory strain Escherichia coli C. Sequencing of bacterial genomes facilitates a comprehensive cataloguing of the urinary virome and reveals phage-host interactions.

IMPORTANCE Bacteriophages are abundant within the human body. However, while some niches have been well surveyed, the phage population within the urinary microbiome is largely unknown. Our study is the first survey of the lysogenic phage population within the urinary microbiota. Most notably, the abundance of prophage exceeds that of the bacteria. Furthermore, many of the prophage sequences identified exhibited no recognizable sequence homology to sequences in data repositories. This suggests a rich diversity of uncharacterized phage species present in the bladder. Additionally, we observed a variation in the abundances of phages between bacteria isolated from asymptomatic “healthy” individuals and those with urinary symptoms, thus suggesting that, like phages within the gut, phages within the bladder may contribute to urinary health.

FOOTNOTES

    • Received 8 December 2017.
    • Accepted 11 January 2018.
    • Accepted manuscript posted online 29 January 2018.
  • Address correspondence to Catherine Putonti, cputonti{at}luc.edu.
  • Citation Miller-Ensminger T, Garretto A, Brenner J, Thomas-White K, Zambom A, Wolfe AJ, Putonti C. 2018. Bacteriophages of the urinary microbiome. J Bacteriol 200:e00738-17. https://doi.org/10.1128/JB.00738-17.

  • Supplemental material for this article may be found at https://doi.org/10.1128/JB.00738-17.

  • Copyright © 2018 American Society for Microbiology.

All Rights Reserved.

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Bacteriophages of the Urinary Microbiome
Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J. Wolfe, Catherine Putonti
Journal of Bacteriology Mar 2018, 200 (7) e00738-17; DOI: 10.1128/JB.00738-17

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Bacteriophages of the Urinary Microbiome
Taylor Miller-Ensminger, Andrea Garretto, Jonathon Brenner, Krystal Thomas-White, Adriano Zambom, Alan J. Wolfe, Catherine Putonti
Journal of Bacteriology Mar 2018, 200 (7) e00738-17; DOI: 10.1128/JB.00738-17
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KEYWORDS

bacteria
bacteriophages
microbiome
prophage
urinary tract
virus

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