Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity

Abstract Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compare...

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Autores principales:	Koji Hosomi, Harumi Ohno, Haruka Murakami, Yayoi Natsume-Kitatani, Kumpei Tanisawa, Soichiro Hirata, Hidehiko Suzuki, Takahiro Nagatake, Tomomi Nishino, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/07d42677e3be4d0297d5529ed4dcc5d1
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spelling	oai:doaj.org-article:07d42677e3be4d0297d5529ed4dcc5d12021-12-02T16:06:08ZMethod for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity10.1038/s41598-017-04511-02045-2322https://doaj.org/article/07d42677e3be4d0297d5529ed4dcc5d12017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-04511-0https://doaj.org/toc/2045-2322Abstract Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e.g., removing GuSCN solution and washing feces with phosphate-buffered saline (PBS) before mechanical lysis), fecal concentration in the GuSCN solution, storage time, and position of fecal subsampling on the 16S rRNA-based analysis of fecal bacteria in GuSCN solution. We found that pretreatment and fecal concentration affected the bacterial composition, and a little change was noted with subsampling position. Based on these results, we propose a basic protocol, including fecal sampling, sample storage, and DNA extraction, for the 16S rRNA-based analysis of bacterial composition in feces suspended in GuSCN solution.Koji HosomiHarumi OhnoHaruka MurakamiYayoi Natsume-KitataniKumpei TanisawaSoichiro HirataHidehiko SuzukiTakahiro NagatakeTomomi NishinoKenji MizuguchiMotohiko MiyachiJun KunisawaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Koji Hosomi Harumi Ohno Haruka Murakami Yayoi Natsume-Kitatani Kumpei Tanisawa Soichiro Hirata Hidehiko Suzuki Takahiro Nagatake Tomomi Nishino Kenji Mizuguchi Motohiko Miyachi Jun Kunisawa Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity
description	Abstract Metagenomic analysis based on the 16S rRNA gene is generally performed to examine the diversity and abundance of commensal bacteria in feces, which is now recognized to be associated with human health and diseases. Guanidine thiocyanate (GuSCN) solution is used as a less onerous way compared with a frozen method to transport and stock fecal samples at room temperature for DNA analysis; however, optimal methods to measure fecal bacterial composition in GuSCN solution remain to be investigated. Here, we examined the influence of various factors such as pretreatment (e.g., removing GuSCN solution and washing feces with phosphate-buffered saline (PBS) before mechanical lysis), fecal concentration in the GuSCN solution, storage time, and position of fecal subsampling on the 16S rRNA-based analysis of fecal bacteria in GuSCN solution. We found that pretreatment and fecal concentration affected the bacterial composition, and a little change was noted with subsampling position. Based on these results, we propose a basic protocol, including fecal sampling, sample storage, and DNA extraction, for the 16S rRNA-based analysis of bacterial composition in feces suspended in GuSCN solution.
format	article
author	Koji Hosomi Harumi Ohno Haruka Murakami Yayoi Natsume-Kitatani Kumpei Tanisawa Soichiro Hirata Hidehiko Suzuki Takahiro Nagatake Tomomi Nishino Kenji Mizuguchi Motohiko Miyachi Jun Kunisawa
author_facet	Koji Hosomi Harumi Ohno Haruka Murakami Yayoi Natsume-Kitatani Kumpei Tanisawa Soichiro Hirata Hidehiko Suzuki Takahiro Nagatake Tomomi Nishino Kenji Mizuguchi Motohiko Miyachi Jun Kunisawa
author_sort	Koji Hosomi
title	Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity
title_short	Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity
title_full	Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity
title_fullStr	Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity
title_full_unstemmed	Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity
title_sort	method for preparing dna from feces in guanidine thiocyanate solution affects 16s rrna-based profiling of human microbiota diversity
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/07d42677e3be4d0297d5529ed4dcc5d1
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Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity

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