Alpha-diversity and microbial community structure of the male urinary microbiota depend on urine sampling method.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
09 12 2021
09 12 2021
Historique:
received:
19
07
2021
accepted:
30
11
2021
entrez:
10
12
2021
pubmed:
11
12
2021
medline:
29
1
2022
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34887510
doi: 10.1038/s41598-021-03292-x
pii: 10.1038/s41598-021-03292-x
pmc: PMC8660768
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
23758Informations de copyright
© 2021. The Author(s).
Références
Eur Urol Oncol. 2020 Dec;3(6):784-788
pubmed: 32345542
Bioinformatics. 2018 Jul 1;34(13):2292-2294
pubmed: 29452334
Eur Urol Focus. 2020 Mar 15;6(2):376-382
pubmed: 30143471
J Clin Microbiol. 2014 Mar;52(3):871-6
pubmed: 24371246
Mol Psychiatry. 2021 Aug;26(8):4277-4287
pubmed: 31988436
J Clin Microbiol. 2019 Feb 27;57(3):
pubmed: 30541935
Int Urol Nephrol. 2018 Jun;50(6):1123-1130
pubmed: 29651696
Am J Obstet Gynecol. 2017 Jan;216(1):55.e1-55.e16
pubmed: 27498309
Nat Commun. 2018 Apr 19;9(1):1557
pubmed: 29674608
PLoS One. 2010 Nov 24;5(11):e14116
pubmed: 21124791
Biol Sex Differ. 2018 Oct 22;9(1):45
pubmed: 30343668
Nature. 2012 Jun 13;486(7402):207-14
pubmed: 22699609
J Urol. 2016 Aug;196(2):435-41
pubmed: 26930255
BMC Microbiol. 2011 Nov 02;11:244
pubmed: 22047020
PLoS One. 2018 Jul 27;13(7):e0201380
pubmed: 30052651
Mol Ecol Resour. 2020 Mar;20(2):415-428
pubmed: 31698527
Arch Microbiol. 1996 Nov;166(5):308-14
pubmed: 8929276
PLoS One. 2010 Jan 06;5(1):e8422
pubmed: 20066050
PLoS One. 2012;7(3):e33865
pubmed: 22457796
PLoS One. 2013 Apr 22;8(4):e61217
pubmed: 23630581
PLoS One. 2011;6(5):e19709
pubmed: 21603636
J Clin Microbiol. 2016 May;54(5):1216-22
pubmed: 26962083
Front Cell Infect Microbiol. 2013 Aug 15;3:41
pubmed: 23967406
Nat Rev Urol. 2019 Feb;16(2):73-74
pubmed: 30510275
J Transl Med. 2012 Aug 28;10:174
pubmed: 22929533
Nat Methods. 2013 Oct;10(10):996-8
pubmed: 23955772
Urology. 2016 Jun;92:26-32
pubmed: 26970449
Int Urogynecol J. 2016 May;27(5):723-33
pubmed: 26423260
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22
pubmed: 20534432
Sci Rep. 2018 Aug 14;8(1):12157
pubmed: 30108246
Front Cell Infect Microbiol. 2018 May 31;8:167
pubmed: 29904624
BMC Urol. 2020 Jan 28;20(1):5
pubmed: 31992287
Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42
pubmed: 24288368
BMC Microbiol. 2012 Sep 13;12:205
pubmed: 22974186
Int Neurourol J. 2020 Mar;24(1):41-51
pubmed: 32252185