Mp34-04 transcriptomic workflow for microbiome profiling of the genitourinary tract

You have accessJournal of UrologyCME1 Apr 2023MP34-04 TRANSCRIPTOMIC WORKFLOW FOR MICROBIOME PROFILING OF THE GENITOURINARY TRACT Jose Agudelo, Sromona Mukherjee, Mangesh Suryavanshi, Ava Adler, Glenn Werneburg, Jacob Knorr, and Aaron Miller Jose AgudeloJose Agudelo More articles by this author , Sromona MukherjeeSromona Mukherjee More articles by this author , Mangesh SuryavanshiMangesh Suryavanshi More articles by this author , Ava AdlerAva Adler More articles by this author , Glenn WerneburgGlenn Werneburg More articles by this author , Jacob KnorrJacob Knorr More articles by this author , and Aaron MillerAaron Miller More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003268.04AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: 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. METHODS: 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 and 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: 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 the organs (Figure 1). A species richness analyses show variable microbial loads between tissue types, which was in part driven by sequencing platform and depth (Figure 2). CONCLUSIONS: Our findings provide evidence of the presence of a diverse microbiome in tissues that span the length of the urinary tract. These results provide a baseline microbial profile of the urobiome that can be used for future studies on health and disease of the genitourinary organs. Source of Funding: Lerner Research Institute © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e460 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Jose Agudelo More articles by this author Sromona Mukherjee More articles by this author Mangesh Suryavanshi More articles by this author Ava Adler More articles by this author Glenn Werneburg More articles by this author Jacob Knorr More articles by this author Aaron Miller More articles by this author Expand All Advertisement PDF downloadLoading ...