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. 2025 Nov 1;31(11):1033-1042.
doi: 10.1097/SPV.0000000000001607.

Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens

Emily S Lukacz  1 , Daniel McDonald  2 , MacKenzie Bryant  2 , Sara Putnam  3 , Kyle Rudser  3 , Caitriona Brennan, Melanie Meister  4 , Cynthia S Fok  5 , Margaret G Mueller  6 , Rob Knight, Linda Brubaker  1 ; Prevention of Lower Urinary Tract Symptoms (PLUS) Research Consortium
Affiliations

Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens

Emily S Lukacz et al. Urogynecology (Phila). .

Abstract

Importance: Population-based research is necessary to understand the relationship between the urobiome and bladder health.

Objective: Using advanced contamination controls and ecological metrics, we aimed to evaluate the concordance of microbiota in self-collected urogenital specimens from home versus a clinical research setting.

Study design: A subset of community-dwelling women was enrolled in a longitudinal cohort study, self-collected urogenital samples at 3 time points: 1-day prior, the day of and during an in-person evaluation. Samples were sequenced with V4 16S rRNA and KatharoSeq removed samples indistinguishable from background contamination. Data were matched to Greengenes2-2022.10 and rarefied to 1000 seqs/sample. Intersample concordance pairs above the KatharoSeq threshold were assessed between samples. Unweighted UniFrac distances, Mantel Pearson correlations, Kruskal-Wallis, and chi-square tests were used for comparisons.

Results: Detectable sequences were obtained in 261 samples from the 114 participants with 186 (71%) above the KatharoSeq threshold. Escherichia_710834, Lactobacillus, and Prevotella were most prevalent. Intersample concordance was determined for samples above the threshold from 38 participants with 2 home samples and 47 with home and clinic samples. Correlations between 2 home and between home and clinic were significant (r = 0.43, P = 0.001; r = 0.362, P = 0.001, respectively). There were no significant differences across time points (X2 = 2.72, P = 0.256).

Conclusions: Home-collected urine samples for urogenital microbiome ecological analysis have sufficient short-term similarity and concordance with self-collected urine samples from a research clinic setting for use in population-based research, which may facilitate inclusion of participants with limited access to clinic-based research.

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Conflict of interest statement

E.S.L. is a consultant/Advisory Board Pathnostics, Royalties UpToDate, and Consultant Tegus. D.M. is a consultant for, and has equity in, BiomeSense, Inc. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies. M.M. is a consult/Advisory Board AbbVie, Inc. C.F. has author royalties in UpToDate and has been a consultant for Medtronic, UroCure. M.M. is an NIH clinical investigator Axonics-Educational Honoraria, Butler Snow-Expert witness. R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., has equity, and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant and scientific advisory board member for DayTwo and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a co-founder of Micronoma and has equity and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego, in accordance with its conflict of interest policies.

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