Urine is the CDC-recommended specimen for STI testing. It was unknown if the
bacterial communities (microbiomes) in urine reflected those in the distal male
urethra. We compared microbiomes of 32 paired urine and urethral swab specimens
obtained from adult men attending an STD clinic, by 16S rRNA PCR and deep
pyrosequencing. Microbiomes of urine and swabs were remarkably similar,
regardless of STI status of the subjects. Thus, urine can be used to
characterize urethral microbiomes when swabs are undesirable, such as in
population-based studies of the urethral microbiome or where multiple sampling
of participants is required
