Simultaneous amplicon analysis of multiple soil samples using MinION sequencing

The diversity and composition of soil microorganisms needs to be understood as they influence ecosystem processes. MinION is a relatively recent next-generation sequencer, which provides the advantage of sequencing long reads. In this study, two types of soil were prepared experimentally to investig...

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Autores principales:	Hiroyuki Kurokochi, Kazutoshi Yoshitake, Ryo Yonezawa, Shuichi Asakawa
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	MinION Soil microbes Amplicon analysis Next-generation sequencing Science Q
Acceso en línea:	https://doaj.org/article/399fab45eeef4c74b387aa0e58e3ddfa
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spelling	oai:doaj.org-article:399fab45eeef4c74b387aa0e58e3ddfa2021-11-14T04:33:09ZSimultaneous amplicon analysis of multiple soil samples using MinION sequencing2215-016110.1016/j.mex.2021.101576https://doaj.org/article/399fab45eeef4c74b387aa0e58e3ddfa2021-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2215016121003666https://doaj.org/toc/2215-0161The diversity and composition of soil microorganisms needs to be understood as they influence ecosystem processes. MinION is a relatively recent next-generation sequencer, which provides the advantage of sequencing long reads. In this study, two types of soil were prepared experimentally to investigate the possibility of simultaneously analyzing multiple environmental samples using MinION. The MinION sequencing of amplicons was adjusted by the different rounds of PCR performed. Soil fungi and bacteria were compared using ITS and 16S rRNA amplicons, respectively. For ITS, the number of reads available for MinION sequencing were simply increased by performing two PCRs and purification using Agencourt AMPure XP. However, the effect of performing PCR twice was not high for 16S rRNA. Therefore, performing PCR twice appears to be effective for analyzing ITS regions. Regarding the number of reads obtained using MinION sequencing, clustering the same sample was possible if a read of ∼2000 bases or more was obtained in 16S rRNA and ITS. Further, information on 80 samples was obtained by performing only one round of MinION sequencing. Thus, MinION sequencing can be used to analyze a large number of samples simultaneously, providing a strong tool for amplicon sequencing.• Soil microbial composition before and after treatment was compared between 16S rRNA and ITS amplicons using MinION sequencing• One PCR amplification and two PCR amplifications were also compared• Information on 80 samples was obtained by performing only one round of MinION sequencingHiroyuki KurokochiKazutoshi YoshitakeRyo YonezawaShuichi AsakawaElsevierarticleMinIONSoil microbesAmplicon analysisNext-generation sequencingScienceQENMethodsX, Vol 8, Iss , Pp 101576- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	MinION Soil microbes Amplicon analysis Next-generation sequencing Science Q
spellingShingle	MinION Soil microbes Amplicon analysis Next-generation sequencing Science Q Hiroyuki Kurokochi Kazutoshi Yoshitake Ryo Yonezawa Shuichi Asakawa Simultaneous amplicon analysis of multiple soil samples using MinION sequencing
description	The diversity and composition of soil microorganisms needs to be understood as they influence ecosystem processes. MinION is a relatively recent next-generation sequencer, which provides the advantage of sequencing long reads. In this study, two types of soil were prepared experimentally to investigate the possibility of simultaneously analyzing multiple environmental samples using MinION. The MinION sequencing of amplicons was adjusted by the different rounds of PCR performed. Soil fungi and bacteria were compared using ITS and 16S rRNA amplicons, respectively. For ITS, the number of reads available for MinION sequencing were simply increased by performing two PCRs and purification using Agencourt AMPure XP. However, the effect of performing PCR twice was not high for 16S rRNA. Therefore, performing PCR twice appears to be effective for analyzing ITS regions. Regarding the number of reads obtained using MinION sequencing, clustering the same sample was possible if a read of ∼2000 bases or more was obtained in 16S rRNA and ITS. Further, information on 80 samples was obtained by performing only one round of MinION sequencing. Thus, MinION sequencing can be used to analyze a large number of samples simultaneously, providing a strong tool for amplicon sequencing.• Soil microbial composition before and after treatment was compared between 16S rRNA and ITS amplicons using MinION sequencing• One PCR amplification and two PCR amplifications were also compared• Information on 80 samples was obtained by performing only one round of MinION sequencing
format	article
author	Hiroyuki Kurokochi Kazutoshi Yoshitake Ryo Yonezawa Shuichi Asakawa
author_facet	Hiroyuki Kurokochi Kazutoshi Yoshitake Ryo Yonezawa Shuichi Asakawa
author_sort	Hiroyuki Kurokochi
title	Simultaneous amplicon analysis of multiple soil samples using MinION sequencing
title_short	Simultaneous amplicon analysis of multiple soil samples using MinION sequencing
title_full	Simultaneous amplicon analysis of multiple soil samples using MinION sequencing
title_fullStr	Simultaneous amplicon analysis of multiple soil samples using MinION sequencing
title_full_unstemmed	Simultaneous amplicon analysis of multiple soil samples using MinION sequencing
title_sort	simultaneous amplicon analysis of multiple soil samples using minion sequencing
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/399fab45eeef4c74b387aa0e58e3ddfa
work_keys_str_mv	AT hiroyukikurokochi simultaneousampliconanalysisofmultiplesoilsamplesusingminionsequencing AT kazutoshiyoshitake simultaneousampliconanalysisofmultiplesoilsamplesusingminionsequencing AT ryoyonezawa simultaneousampliconanalysisofmultiplesoilsamplesusingminionsequencing AT shuichiasakawa simultaneousampliconanalysisofmultiplesoilsamplesusingminionsequencing
_version_	1718429950348886016

Simultaneous amplicon analysis of multiple soil samples using MinION sequencing

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