Benchmarking DNA isolation kits used in analyses of the urinary microbiome.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
17 03 2021
17 03 2021
Historique:
received:
12
09
2020
accepted:
02
03
2021
entrez:
18
3
2021
pubmed:
19
3
2021
medline:
21
10
2021
Statut:
epublish
Résumé
The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
Identifiants
pubmed: 33731788
doi: 10.1038/s41598-021-85482-1
pii: 10.1038/s41598-021-85482-1
pmc: PMC7969918
doi:
Substances chimiques
DNA, Bacterial
0
Types de publication
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6186Subventions
Organisme : NIDDK NIH HHS
ID : K01 DK116706
Pays : United States
Organisme : NIDDK NIH HHS
ID : K12 DK100024
Pays : United States
Organisme : NIA NIH HHS
ID : P30 AG028716
Pays : United States
Organisme : NIA NIH HHS
ID : R03 AG060082
Pays : United States
Organisme : NIDDK NIH HHS
ID : K23 DK110417
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002369
Pays : United States
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