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This study sought to conduct a systematic review of the role of the microbiota in urinary chronic pelvic pain syndrome (UCPPS).<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We searched Embase, Scopus, Web of Science, and PubMed with no time, language, or study type restrictions until December 1, 2023. The JBI Appraisal Tool was used to assess the quality of the studies. Study selection followed the PRISMA statement. Studies addressing microbiome variations among patients suffering from interstitial cystitis\/bladder pain syndrome (IC\/BPS) or chronic prostatitis\/chronic pelvic pain syndrome (CP\/CPPS) and a control group were considered eligible.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>A total of 21 studies (1 UCPPS, 12 IC\/BPS, and 8 CP\/CPPS) comprising 1125 patients were enrolled in our final data synthesis. It has been shown that the reduced diversity and discrepant composition of the gut microbiota may partly be attributed to the UCPPS pathogenesis. In terms of urine microbiota, some operational taxonomic units were shown to be elevated, while others became less abundant. Furthermore, various bacteria and fungi are linked to specific clinical features. Few investigations denied UCPPS as a dysbiotic condition.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Urinary and intestinal microbiota appear to be linked with UCPPS, comprising IC\/BPS and CP\/CPPS. However, given the substantial disparity of published studies, a battery of prospective trials is required to corroborate these findings.<\/jats:p><\/jats:sec>","DOI":"10.1002\/nau.25550","type":"journal-article","created":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T06:08:50Z","timestamp":1720764530000},"page":"1859-1882","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["A systematic and comprehensive review of the role of microbiota in urinary chronic pelvic pain syndrome"],"prefix":"10.1002","volume":"43","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-6384-7500","authenticated-orcid":false,"given":"Negin","family":"Hashemi","sequence":"first","affiliation":[{"name":"Pharmaceutical Analysis Research Center, Faculty of Pharmacy Tabriz University of Medical Sciences Tabriz 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