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

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 as...

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Autores principales: Hrbacek, Jan, Morais, Daniel, Cermak, Pavel, Hanacek, Vitezslav, Zachoval, Roman
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8660768/
https://www.ncbi.nlm.nih.gov/pubmed/34887510
http://dx.doi.org/10.1038/s41598-021-03292-x
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author Hrbacek, Jan
Morais, Daniel
Cermak, Pavel
Hanacek, Vitezslav
Zachoval, Roman
author_facet Hrbacek, Jan
Morais, Daniel
Cermak, Pavel
Hanacek, Vitezslav
Zachoval, Roman
author_sort Hrbacek, Jan
collection PubMed
description 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.
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spelling pubmed-86607682021-12-13 Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method Hrbacek, Jan Morais, Daniel Cermak, Pavel Hanacek, Vitezslav Zachoval, Roman Sci Rep Article 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. Nature Publishing Group UK 2021-12-09 /pmc/articles/PMC8660768/ /pubmed/34887510 http://dx.doi.org/10.1038/s41598-021-03292-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Hrbacek, Jan
Morais, Daniel
Cermak, Pavel
Hanacek, Vitezslav
Zachoval, Roman
Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
title Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
title_full Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
title_fullStr Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
title_full_unstemmed Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
title_short Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
title_sort alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8660768/
https://www.ncbi.nlm.nih.gov/pubmed/34887510
http://dx.doi.org/10.1038/s41598-021-03292-x
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