Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method

0559328 - MBÚ 2023 RIV GB eng J - Journal Article
Hrbáček, J. - Morais, Daniel - Čermák, P. - Hanáček, V. - Zachoval, R.
Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method.
Scientific Reports. Roč. 11, č. 1 (2021), č. článku 23758. ISSN 2045-2322. E-ISSN 2045-2322
Institutional support: RVO:61388971
Keywords : Alpha‑diversity * urinary microbiota * microbiota studies
OECD category: Microbiology
Impact factor: 4.997, year: 2021
Method of publishing: Open access
https://www.nature.com/articles/s41598-021-03292-x

Considerable variation exists in the methodology of urinary microbiota studies published so far including the cornerstone of any biomedical analysis: sample collection. The aim of this study was to compare the urinary microbiota of first-catch voided urine (FCU), mid-stream voided urine (MSU) and aseptically catheterised urine in men and define the most suitable urine sampling method. Forty-nine men (mean age 71.3 years) undergoing endoscopic urological procedures 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 in three of five alpha-diversity measures (ANOVA, p < 0.05): estimated number of operational taxonomic units, Chao1 and abundance-based coverage estimators. Beta-diversity comparisons using the PIME method (Prevalence Interval for Microbiome Evaluation) resulted in clustering of urine samples according to the mode of sampling. EQUC detected cultivable bacteria in 30/31 (97%) FCU and 27/31 (87%) MSU samples. Only 4/31 (13%) of catheterised urine samples showed bacterial growth. Urine samples obtained by transurethral catheterisation under aseptic conditions seem to differ from spontaneously voided urine samples. Whether the added value of a more exact reflection of the bladder microbiota free from urethral contamination outweighs the invasiveness of urethral catheterisation remains to be determined.
Permanent Link: https://hdl.handle.net/11104/0332658