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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

Inter-subject variability in 16S rRNA clones in urine.4,386-16S rRNA Urine sequences were sorted to the Phyla level using RDP Classifier at 90% confidence cutoff [23]. Subjects are indicated below bars on the X-axis and the percents of clones corresponding to specific phyla are indicated on the Y-axis. STI status of the subjects is indicated below the X-axis.
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pone-0014116-g001: Inter-subject variability in 16S rRNA clones in urine.4,386-16S rRNA Urine sequences were sorted to the Phyla level using RDP Classifier at 90% confidence cutoff [23]. Subjects are indicated below bars on the X-axis and the percents of clones corresponding to specific phyla are indicated on the Y-axis. STI status of the subjects is indicated below the X-axis.

Mentions: To identify bacterial taxa, which could represent the “core” urine microbiome 16S rRNA sequences, were classified to the phylum level, according to RDP II taxonomy, and compared. Seven phyla were identified in total. Sequences corresponding to five bacterial phyla including Firmicutes (52.6%), Actinobacteria (18.7%), Fusobacteria (10.0%), Proteobacteria (9.4%) and Bacteroidetes (7.4%) were frequently detected, whereas sequences corresponding to Tenericutes (1.8%) and TM7 (<0.1%) were less abundant. The distribution of these phyla differed markedly among the urine specimens (Figure 1). Firmicutes were present in all specimens and Actinobacteria and Proteobacteria were each present in 18/19. Proportions of total sequences in urine corresponding to these phyla (where present) ranged from 3.5–93.1%, 0.4–90.3% and 1.3–62.2% for Firmicutes, Actinobacteria and Proteobacteria, respectively. Bacteroidetes and Tenericutes were identified in 15/19 and 9/19 urine specimens but never constituted more than 25% of total sequences in any urine. In contrast, Fusobacteria were only detected in 9/19 urine specimens but accounted for a significant proportion of total sequences (0.4–47.8%, mean 18.9%, SD 15.4%) when present. TM7 was detected in 3 urine in which it accounted for 0.3–1.5% of the total sequences. These results indicated that there is substantial intra-individual variation in urine microbiomes even at the phylum level.


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)

Inter-subject variability in 16S rRNA clones in urine.4,386-16S rRNA Urine sequences were sorted to the Phyla level using RDP Classifier at 90% confidence cutoff [23]. Subjects are indicated below bars on the X-axis and the percents of clones corresponding to specific phyla are indicated on the Y-axis. STI status of the subjects is indicated below the X-axis.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0014116-g001: Inter-subject variability in 16S rRNA clones in urine.4,386-16S rRNA Urine sequences were sorted to the Phyla level using RDP Classifier at 90% confidence cutoff [23]. Subjects are indicated below bars on the X-axis and the percents of clones corresponding to specific phyla are indicated on the Y-axis. STI status of the subjects is indicated below the X-axis.
Mentions: To identify bacterial taxa, which could represent the “core” urine microbiome 16S rRNA sequences, were classified to the phylum level, according to RDP II taxonomy, and compared. Seven phyla were identified in total. Sequences corresponding to five bacterial phyla including Firmicutes (52.6%), Actinobacteria (18.7%), Fusobacteria (10.0%), Proteobacteria (9.4%) and Bacteroidetes (7.4%) were frequently detected, whereas sequences corresponding to Tenericutes (1.8%) and TM7 (<0.1%) were less abundant. The distribution of these phyla differed markedly among the urine specimens (Figure 1). Firmicutes were present in all specimens and Actinobacteria and Proteobacteria were each present in 18/19. Proportions of total sequences in urine corresponding to these phyla (where present) ranged from 3.5–93.1%, 0.4–90.3% and 1.3–62.2% for Firmicutes, Actinobacteria and Proteobacteria, respectively. Bacteroidetes and Tenericutes were identified in 15/19 and 9/19 urine specimens but never constituted more than 25% of total sequences in any urine. In contrast, Fusobacteria were only detected in 9/19 urine specimens but accounted for a significant proportion of total sequences (0.4–47.8%, mean 18.9%, SD 15.4%) when present. TM7 was detected in 3 urine in which it accounted for 0.3–1.5% of the total sequences. These results indicated that there is substantial intra-individual variation in urine microbiomes even at the phylum level.

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