Abstract
While once believed to represent a sterile environment, the human urinary tract harbors a unique cellular microbiota. We sought to determine whether the human urinary tract also is home to viral communities whose membership might reflect urinary tract health status. We recruited and sampled urine from 20 subjects, 10 subjects with urinary tract infections (UTIs) and 10 without UTIs, and found viral communities in the urine of each subject group. Most of the identifiable viruses were bacteriophage, but eukaryotic viruses also were identified in all subjects. We found reads from human papillomaviruses (HPVs) in 95% of the subjects studied, but none were found to be high-risk genotypes that are associated with cervical and rectal cancers. We verified the presence of some HPV genotypes by quantitative PCR. Some of the HPV genotypes identified were homologous to relatively novel and uncharacterized viruses that previously have been detected on skin in association with cancerous lesions, while others may be associated with anal and genital warts. On a community level, there was no association between the membership or diversity of viral communities based on urinary tract health status. While more data are still needed, detection of HPVs as members of the human urinary virome using viral metagenomics represents a non-invasive technique that could augment current screening techniques to detect low-risk HPVs in the genitourinary tracts of humans.
Highlights
The presence of microbes inhabiting the human urinary tract has generally been associated with urinary tract infections (UTIs), but recent studies have demonstrated that the urine has its own unique microbiota even in the absence of UTIs (Nelson et al, 2010; Siddiqui et al, 2011; Wolfe et al, 2012)
While a threshold concentration of 103 Colony Forming Units (CFU) per ml of urine accompanied with lower urinary tract symptoms is required for a UTI diagnosis, there are some pathogens that are not detected by standard microbiological culture techniques (Rubin et al, 1992)
We found that there were approximately 107 virus-like particles (VLPs) in the urine of UTI+ and UTI− subjects, which is an order of magnitude lower than we have previously found in human saliva (Pride et al, 2012)
Summary
The presence of microbes inhabiting the human urinary tract has generally been associated with urinary tract infections (UTIs), but recent studies have demonstrated that the urine has its own unique microbiota even in the absence of UTIs (Nelson et al, 2010; Siddiqui et al, 2011; Wolfe et al, 2012). Many of these microbiota may not be culturable using conventional culture techniques, but the presence of a diverse microbiota in human urine has highlighted the need to understand whether there is a role for these communities of microbes in urinary tract health or disease. Disturbances to the urinary tract microbiota can be recognized in the presence of pathogens (Pearce et al, 2014), but it is not yet clear how long it takes for the urinary tract to recover its normal microbiota after both pathogen-mediated disturbances and antibiotic therapy
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