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BackgroundNumerous studies have emerged in the past decade investigating human urinary microbiota. Alterations in the microbial composition of urine have been linked to structural and functional abnormalities of the lower urinary tract. There has been considerable variation in the methodology of the studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to describe the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and find the most suitable approach to urine sample collection for the purpose of male urinary microbiota investigations.ResultsForty-nine men (mean age 71.3 years) undergoing endoscopic procedures in our Department of Urology were enrolled in the study. Each of them contributed three samples: first-catch urine (FCU), mid-stream urine (MSU) and a catheterised urine sample. The samples were subjected to next-generation sequencing (NGS, n=35) and expanded quantitative urine culture (EQUC, n=31). Using NGS, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant phyla in our population. The most abundant genera (in order of relative abundance) included: Prevotella, Veillonella, Streptococcus, Porphyromonas, Campylobacter, Pseudomonas, Staphylococcus, Ezakiella, Escherichia and Dialister. Eighty-two of 105 samples were dominated by a single genus. FCU, MSU and catheterised urine samples differed significantly using ANOVA in three out of five alpha-diversity measures (p |
