Prospective examination of the changes in the urinary microbiome induced by transrectal biopsy of the prostate using 16S rRNA gene analysis




To prospectively examine the changes in microbiota within the urinary tract after transrectal prostate biopsy.

Materials and methods

Data, urine, and fecal samples prospectively collected from 30 patients before and after transrectal biopsy of the prostate. DNA was extracted from urine collected after a prostate massage before and after prostate biopsy, and from fecal samples collected before the biopsy. We sequenced DNA using the bacterial 16S rRNA high-throughput next-generation sequencing and analyzed changes in microbial profiles for taxonomy comparison between samples.


Pre-biopsy urinary microbial profiles contained Lactobacillus and Staphylococcus bacteria. Post-biopsy urinary microbial profiles included lower levels of Lactobacillus and higher levels of Prevotella bacteria. Bacteroides bacteria were predominant in fecal samples. We identified two clustering patterns containing both pre- and post-biopsy urine samples. Cluster 1 had a urine cluster pattern that was distinct from fecal, whereas cluster 2 was similar to fecal. We observed two different modes of microbial changes, 11 patients had both of their urine (pre and post) samples associated with a particular cluster group, whereas others (n = 15) had movement between clusters 1 and 2 following the biopsy procedure. Four patient’s post-biopsy urine microbial profiles clustered very tightly to the fecal microbial profile.


We describe two models of change in the urinary tract microbiota after prostate biopsy using 16S RNA gene analysis. Further research to determine what controls changes in the urinary microbiota after prostate biopsy can help us understand why some patients are more susceptible to develop post-biopsy infections.

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This work was supported by Southern Illinois University research grant.

Author information




SA: Study design, data collection and interpretation, manuscript writing, and supervision. Ahmed El-Zawahry MD, PhD: Study design, data collection and interpretation, manuscript writing. Danuta Dynda MD: Regulatory coordination and patient consenting, data collection and analysis. Kevin McVary MD: Data analysis, critical revision of the paper, and supervision. Mallory Karr: Data analysis and interpretation, manuscript writing. Andrea Braundmeier-Fleming PhD: Study design, data analysis and interpretation, manuscript writing, and supervision.

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Correspondence to Shaheen Alanee.

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Alanee, S., El-Zawahry, A., Dynda, D. et al. Prospective examination of the changes in the urinary microbiome induced by transrectal biopsy of the prostate using 16S rRNA gene analysis. Prostate Cancer Prostatic Dis 22, 446–452 (2019).

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