Presented by: Jose Agudelo MD
Cleveland Clinic

Introduction

Multiple studies have revealed the presence of viable microorganisms in the urinary tract designated as the urobiome.  Dysbiosis of the urobiome has been associated with a number of urologic diseases. The purpose of the present study was to characterize and compare the trans-domain microbiome in diverse genitourinary tract tissue. 

Materials

The sequence read archive (SRA) was searched for human transcriptomic data derived from human genitourinary tissue. An automated workflow was developed and run for studies that fit the above criteria, as follows: downloading raw sequencing data, filtering, and mapping to the GRCh38 human genome. Then nonhosts reads were mapped to a database that contains >45,000 full-length Prokaryotic, Protozoan, Viral, and Fungal genomes downloaded from the NCBI. The resulting microbial taxonomic profiles were used to quantify differences and similarities in the microbial profiles of different regions of the genitourinary tract.  Additionally, when applicable, patient-specific analyses were conducted to determine the factors that shape the urobiome and possible disease-specific dysbioses.

Results

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Ten studies fit our criteria and included samples from urine, semen, prostate tumor, upper tract urothelium, testicle, kidney, bladder tumor, and laser micro dissected tubuli and glomeruli. Five studies used shotgun metagenomics, with four RNA-seq, and one exome-seq. We were able to identify taxa from all domains in all tissue types, with Prokaryotes dominating the microbiome in all tissues (Figure 1). A trans-domain species richness analyses show variable microbial loads between tissue types, which was in part driven by sequencing platform and depth.

Conclusion

Our findings provide evidence of the presence of a diverse microbiome in tissues that span the length of the genitourinary tract. These results provide a baseline microbial profile of the urobiome that can be used for future targeted studies on health and disease of the genitourinary organs.

Funding

Lerner Research Institute

Lead Authors

Sromona Mukherjee,
Cleveland Clinic

Mangesh Suryavanshi,
Cleveland Clinic

Ava Adler,
Cleveland Clinic

Thien Dang,
Cleveland Clinic

Aaron Miller,
Cleveland Clinic