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Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.

Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD - PLoS ONE (2010)

Bottom Line: All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina.The same taxa were rare in STI negative individuals.Our findings suggest that the composition of male urine microbiomes is related to STI.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Indiana University, Bloomington, Indiana, USA. nelsonde@indiana.edu

ABSTRACT

Background: The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization of the male urethra might impact risk of sexually transmitted infection (STI). Previous cultivation-dependent studies showed that a variety of non-pathogenic bacteria colonize the urethra but did not thoroughly characterize these microbiomes or establish links between the compositions of urethral microbiomes and STI.

Methodology/findings: Here, we used 16S rRNA PCR and sequencing to identify bacteria in urine specimens collected from men who lacked symptoms of urethral inflammation but who differed in status for STI. All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina. Uncultivated bacteria associated with female genital tract pathology were abundant in specimens from men who had STI.

Conclusions: Urine microbiomes from men with STI were dominated by fastidious, anaerobic and uncultivated bacteria. The same taxa were rare in STI negative individuals. Our findings suggest that the composition of male urine microbiomes is related to STI.

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Related in: MedlinePlus

Hierarchical clustering of urine microbiomes.Genus names corresponding to terminal taxa depicted in the heat map are listed to the right of the figure. Subjects are listed at the bottom. Intensity of the coloration of cells in the heat map indicates the extent of correlation of different urine samples. Dendograms at the top and right of the heat map indicate relationships of microbiomes and genera, respectively. The top infection color bar indicates STI (labeled as YES) or non-STI (labeled as NONE) participants.
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pone-0014116-g002: Hierarchical clustering of urine microbiomes.Genus names corresponding to terminal taxa depicted in the heat map are listed to the right of the figure. Subjects are listed at the bottom. Intensity of the coloration of cells in the heat map indicates the extent of correlation of different urine samples. Dendograms at the top and right of the heat map indicate relationships of microbiomes and genera, respectively. The top infection color bar indicates STI (labeled as YES) or non-STI (labeled as NONE) participants.

Mentions: To identify potential associations between bacterial taxa the urine microbiomes were hierarchically clustered and genera were weighted to reflect their abundance. Figure 2 depicts clustering results produced using pair-wise Spearman's rank correlation coefficients among all the genera from urine. The first cluster (Fig. 2, from the left end) contains eight urine specimens, all of which were positive for one or more STI by specific nucleic acid amplification tests and/or by the presence of sequences corresponding to known sexually transmitted pathogens (Table S3). All eight specimens in this cluster contained Prevotella and Sneathia spp., Prevotella was only detected in 2 specimens outside this group, and Sneathia spp. were unique to this group. Other frequent and or abundant genera in this group included Dialister (7/8), Gemella (7/8), and Atopobium (5/8). The second cluster contained two specimens and the majority of sequences in both of these were Lactobacillus iners. One of these was also positive for Mycoplasma spp. There are nine specimens in the third cluster. Although there was substantial diversity comparing these urine, one or more of Corynebacteria, Propionobacteria, Staphylococcus and or Streptococci spp. were dominant. Approximately 5% of the sequences from one urine (Urine 13) corresponded to a reference strain of N. gonorrhoeae (>99% identical), but this was the only STI positive urine in this cluster (Table S3).


Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.

Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD - PLoS ONE (2010)

Hierarchical clustering of urine microbiomes.Genus names corresponding to terminal taxa depicted in the heat map are listed to the right of the figure. Subjects are listed at the bottom. Intensity of the coloration of cells in the heat map indicates the extent of correlation of different urine samples. Dendograms at the top and right of the heat map indicate relationships of microbiomes and genera, respectively. The top infection color bar indicates STI (labeled as YES) or non-STI (labeled as NONE) participants.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2991352&req=5

pone-0014116-g002: Hierarchical clustering of urine microbiomes.Genus names corresponding to terminal taxa depicted in the heat map are listed to the right of the figure. Subjects are listed at the bottom. Intensity of the coloration of cells in the heat map indicates the extent of correlation of different urine samples. Dendograms at the top and right of the heat map indicate relationships of microbiomes and genera, respectively. The top infection color bar indicates STI (labeled as YES) or non-STI (labeled as NONE) participants.
Mentions: To identify potential associations between bacterial taxa the urine microbiomes were hierarchically clustered and genera were weighted to reflect their abundance. Figure 2 depicts clustering results produced using pair-wise Spearman's rank correlation coefficients among all the genera from urine. The first cluster (Fig. 2, from the left end) contains eight urine specimens, all of which were positive for one or more STI by specific nucleic acid amplification tests and/or by the presence of sequences corresponding to known sexually transmitted pathogens (Table S3). All eight specimens in this cluster contained Prevotella and Sneathia spp., Prevotella was only detected in 2 specimens outside this group, and Sneathia spp. were unique to this group. Other frequent and or abundant genera in this group included Dialister (7/8), Gemella (7/8), and Atopobium (5/8). The second cluster contained two specimens and the majority of sequences in both of these were Lactobacillus iners. One of these was also positive for Mycoplasma spp. There are nine specimens in the third cluster. Although there was substantial diversity comparing these urine, one or more of Corynebacteria, Propionobacteria, Staphylococcus and or Streptococci spp. were dominant. Approximately 5% of the sequences from one urine (Urine 13) corresponded to a reference strain of N. gonorrhoeae (>99% identical), but this was the only STI positive urine in this cluster (Table S3).

Bottom Line: All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina.The same taxa were rare in STI negative individuals.Our findings suggest that the composition of male urine microbiomes is related to STI.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Indiana University, Bloomington, Indiana, USA. nelsonde@indiana.edu

ABSTRACT

Background: The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization of the male urethra might impact risk of sexually transmitted infection (STI). Previous cultivation-dependent studies showed that a variety of non-pathogenic bacteria colonize the urethra but did not thoroughly characterize these microbiomes or establish links between the compositions of urethral microbiomes and STI.

Methodology/findings: Here, we used 16S rRNA PCR and sequencing to identify bacteria in urine specimens collected from men who lacked symptoms of urethral inflammation but who differed in status for STI. All of the urine samples contained multiple bacterial genera and many contained taxa that colonize the human vagina. Uncultivated bacteria associated with female genital tract pathology were abundant in specimens from men who had STI.

Conclusions: Urine microbiomes from men with STI were dominated by fastidious, anaerobic and uncultivated bacteria. The same taxa were rare in STI negative individuals. Our findings suggest that the composition of male urine microbiomes is related to STI.

Show MeSH
Related in: MedlinePlus