Benchmarking DNA isolation kits used in analyses of the urinary microbiome

Abstract 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 to...

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Autores principales:	Lisa Karstens, Nazema Y. Siddiqui, Tamara Zaza, Alecsander Barstad, Cindy L. Amundsen, Tatyana A. Sysoeva
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/faee88c93c1744bb98cc15c2e2d352cd
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spelling	oai:doaj.org-article:faee88c93c1744bb98cc15c2e2d352cd2021-12-02T13:18:01ZBenchmarking DNA isolation kits used in analyses of the urinary microbiome10.1038/s41598-021-85482-12045-2322https://doaj.org/article/faee88c93c1744bb98cc15c2e2d352cd2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85482-1https://doaj.org/toc/2045-2322Abstract 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.Lisa KarstensNazema Y. SiddiquiTamara ZazaAlecsander BarstadCindy L. AmundsenTatyana A. SysoevaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lisa Karstens Nazema Y. Siddiqui Tamara Zaza Alecsander Barstad Cindy L. Amundsen Tatyana A. Sysoeva Benchmarking DNA isolation kits used in analyses of the urinary microbiome
description	Abstract 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.
format	article
author	Lisa Karstens Nazema Y. Siddiqui Tamara Zaza Alecsander Barstad Cindy L. Amundsen Tatyana A. Sysoeva
author_facet	Lisa Karstens Nazema Y. Siddiqui Tamara Zaza Alecsander Barstad Cindy L. Amundsen Tatyana A. Sysoeva
author_sort	Lisa Karstens
title	Benchmarking DNA isolation kits used in analyses of the urinary microbiome
title_short	Benchmarking DNA isolation kits used in analyses of the urinary microbiome
title_full	Benchmarking DNA isolation kits used in analyses of the urinary microbiome
title_fullStr	Benchmarking DNA isolation kits used in analyses of the urinary microbiome
title_full_unstemmed	Benchmarking DNA isolation kits used in analyses of the urinary microbiome
title_sort	benchmarking dna isolation kits used in analyses of the urinary microbiome
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/faee88c93c1744bb98cc15c2e2d352cd
work_keys_str_mv	AT lisakarstens benchmarkingdnaisolationkitsusedinanalysesoftheurinarymicrobiome AT nazemaysiddiqui benchmarkingdnaisolationkitsusedinanalysesoftheurinarymicrobiome AT tamarazaza benchmarkingdnaisolationkitsusedinanalysesoftheurinarymicrobiome AT alecsanderbarstad benchmarkingdnaisolationkitsusedinanalysesoftheurinarymicrobiome AT cindylamundsen benchmarkingdnaisolationkitsusedinanalysesoftheurinarymicrobiome AT tatyanaasysoeva benchmarkingdnaisolationkitsusedinanalysesoftheurinarymicrobiome
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Benchmarking DNA isolation kits used in analyses of the urinary microbiome

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