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Recent studies suggest that microbiota can serve as predictors for fertility treatment outcomes. Our objective was to investigate the degree of similarity in microbial composition between patient-collected urine and vaginal samples in a subfertile population. We enrolled women of reproductive age (20\u201344 years) diagnosed with subfertility and requiring in vitro fertilization (IVF) or IVF with intracytoplasmic sperm injection (IVF-ICSI) treatment. They self-collected both mid-stream urine samples and vaginal swabs before commencing the IVF or IVF-ICSI procedure. All samples were analysed using the intergenic spacer profiling (IS-pro) technique, a rapid clinical microbiota analysis tool. The main outcome measures were the degree of similarity of microbial composition between the two different, but simultaneously collected, samples. Our findings revealed a high correlation (R squared of 0.78) in microbiota profiles between paired urine and vaginal samples from individual patients. Nevertheless, the urinary microbiota profiles contained fewer species compared to the vaginal microbiota, resulting in minor but distinguishable differences. Furthermore, different subfertility diagnoses appeared to be associated with differences in microbial profiles. A noteworthy observation was the exclusive presence of Escherichia coli (E. coli) in both samples of women diagnosed with male factor subfertility. In conclusion, since urinary microbiota profiles seem to represent a diluted version of the vaginal microbiota, vaginal microbiome sampling to predict fertility treatment outcome seems preferable. To enhance the success of fertility treatments, further research is needed to gain deeper insights into a putative causal role of microbiota in the mechanisms of subfertility.<\/jats:p>","DOI":"10.3390\/microorganisms12091789","type":"journal-article","created":{"date-parts":[[2024,8,29]],"date-time":"2024-08-29T08:01:47Z","timestamp":1724918507000},"page":"1789","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Clinical Applicability of Microbiota Sampling in a Subfertile Population: Urine versus Vagina"],"prefix":"10.3390","volume":"12","author":[{"given":"Rivka","family":"Koedooder","sequence":"first","affiliation":[{"name":"Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Schoenmakers","sequence":"additional","affiliation":[{"name":"Division Obstetrics, Department of Obstetrics and Gynecology, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Singer","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VUmc, 1081 HV Amsterdam, The Netherlands"},{"name":"Tubascan (Spin-Off Company), Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VUmc, 1081 HV Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4005-7680","authenticated-orcid":false,"given":"Martine","family":"Bos","sequence":"additional","affiliation":[{"name":"inBiome, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Poort","sequence":"additional","affiliation":[{"name":"inBiome, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Savelkoul","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VUmc, 1081 HV Amsterdam, The Netherlands"},{"name":"Department of Medical Microbiology, Infectious Diseases & Infection Prevention, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Servaas","family":"Morr\u00e9","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad 211007, India"},{"name":"Institute of Public Health Genomics, Department of Genetics and Cell Biology, Research Institute for Oncology and Reproduction, Faculty of Health, Medicine & Life Sciences, University of Maastricht, 6211 LK Maastricht, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2832-1255","authenticated-orcid":false,"given":"Jonathan","family":"de Jonge","sequence":"additional","affiliation":[{"name":"ARTPred B.V., 1438 AX Oude Meer, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5128-5411","authenticated-orcid":false,"given":"Dries","family":"Budding","sequence":"additional","affiliation":[{"name":"inBiome, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joop","family":"Laven","sequence":"additional","affiliation":[{"name":"Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,8,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Zi\u0119tek, M., Celewicz, Z., and Szczuko, M. 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