{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T06:02:08Z","timestamp":1785391328403,"version":"3.55.0"},"reference-count":101,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T00:00:00Z","timestamp":1785369600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>The recognition of the urinary microbiome (urobiome) has challenged the long-standing paradigm of urinary tract sterility, revealing diverse microbial communities associated with both urinary health and disease. However, the characterization of the urobiome remains highly variable across studies, particularly due to the low-biomass nature of urine samples and the strong influence of methodological bias. In this Mini Review, we examine how factors such as sample collection methods, contamination dynamics, DNA extraction protocols, sequencing approaches, and bioinformatic pipelines shape microbial profiles and contribute to inconsistencies in microbiome\u2013disease associations. We further discuss the limitations of traditional culture-based diagnostics, which fail to detect many microorganisms identified through sequencing-based approaches, and highlight the need for standardized, contamination-aware, and function-oriented frameworks. Finally, we explore the potential of integrated multi-omics strategies to improve the reliability, reproducibility, and clinical relevance of urobiome research in urinary tract health and disease.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1851926","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T05:40:21Z","timestamp":1785390021000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Methodological bias shapes the interpretation of the urinary microbiome in low-biomass systems"],"prefix":"10.3389","volume":"17","author":[{"given":"Viviana","family":"M\u00e9ndez-Sacta","sequence":"first","affiliation":[{"name":"Faculty of Medical Sciences, University of Cuenca","place":["Cuenca, Ecuador"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Solmayra","family":"Agreda Orellana","sequence":"additional","affiliation":[{"name":"Faculty of Medical Sciences, University of Cuenca","place":["Cuenca, Ecuador"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luz Mar\u00eda","family":"Ayavaca-Tapia","sequence":"additional","affiliation":[{"name":"Faculty of Medical Sciences, University of Cuenca","place":["Cuenca, Ecuador"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yomaira Yolanda","family":"Guti\u00e9rrez Le\u00f3n","sequence":"additional","affiliation":[{"name":"Faculty of Medical Sciences, University of Cuenca","place":["Cuenca, Ecuador"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William","family":"Calero-C\u00e1ceres","sequence":"additional","affiliation":[{"name":"Biotechnology Program, Department of Food and Biotechnology Science and Engineering, Universidad T\u00e9cnica de Ambato","place":["Ambato, Ecuador"]},{"name":"UTA-RAM-One Health, Group for Universal Advance in Bioscience, Department of Food and Biotechnology Science and Engineering, Universidad T\u00e9cnica de Ambato","place":["Ambato, Ecuador"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1186\/S12866-021-02391-Z","article-title":"ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples","volume":"21","author":"Abellan-Schneyder","year":"2021","journal-title":"BMC Microbiol. 2021 21:1"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e0210306","DOI":"10.1371\/journal.pone.0210306","article-title":"Optimization of DNA extraction from human urinary samples for mycobiome community profiling","volume":"14","author":"Ackerman","year":"2019","journal-title":"PLoS One"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1016\/j.chom.2020.06.022","article-title":"The urinary tract microbiome in older women exhibits host genetic and environmental influences","volume":"28","author":"Adebayo","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s40168-021-01204-9","article-title":"Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states","volume":"10","author":"Adu-Oppong","year":"2022","journal-title":"Microbiome"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"5","DOI":"10.4137\/ebo.s36436","article-title":"Metagenomics, Metatranscriptomics, and metabolomics approaches for microbiome analysis","author":"Aguiar-Pulido","year":"2016","journal-title":"Evol. 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