Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens

Authors:
  • CBCaitriona Brennan
    Caitriona Brennan
  • RKRob Knight
    Rob Knight
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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 ( X 2 = 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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