The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.

Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts....

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Autores principales:	Jonas Ghyselinck, Stefan Pfeiffer, Kim Heylen, Angela Sessitsch, Paul De Vos
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ea3b8b9b92254950b771d94543b9bc2a
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spelling	oai:doaj.org-article:ea3b8b9b92254950b771d94543b9bc2a2021-11-18T08:59:10ZThe effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.1932-620310.1371/journal.pone.0071360https://doaj.org/article/ea3b8b9b92254950b771d94543b9bc2a2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23977026/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts. All the unknowns associated with sequencing data, i.e. primer coverage rate, phylogeny, OTU-richness and taxonomic assignment, were therefore implemented in one study for ten well established universal primers (338f/r, 518f/r, 799f/r, 926f/r and 1062f/r) targeting dispersed regions of the bacterial 16S rRNA gene. All analyses were performed on nearly full length and in silico generated short read sequence libraries containing 1175 sequences that were carefully chosen as to present a representative substitute of the SILVA SSU database. The 518f and 799r primers, targeting the V4 region of the 16S rRNA gene, were found to be particularly suited for short read sequencing studies, while the primer 1062r, targeting V6, seemed to be least reliable. Our results will assist scientists in considering whether the best option for their study is to select the most informative primer, or the primer that excludes interferences by host-organelle DNA. The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment.Jonas GhyselinckStefan PfeifferKim HeylenAngela SessitschPaul De VosPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 8, p e71360 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jonas Ghyselinck Stefan Pfeiffer Kim Heylen Angela Sessitsch Paul De Vos The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
description	Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts. All the unknowns associated with sequencing data, i.e. primer coverage rate, phylogeny, OTU-richness and taxonomic assignment, were therefore implemented in one study for ten well established universal primers (338f/r, 518f/r, 799f/r, 926f/r and 1062f/r) targeting dispersed regions of the bacterial 16S rRNA gene. All analyses were performed on nearly full length and in silico generated short read sequence libraries containing 1175 sequences that were carefully chosen as to present a representative substitute of the SILVA SSU database. The 518f and 799r primers, targeting the V4 region of the 16S rRNA gene, were found to be particularly suited for short read sequencing studies, while the primer 1062r, targeting V6, seemed to be least reliable. Our results will assist scientists in considering whether the best option for their study is to select the most informative primer, or the primer that excludes interferences by host-organelle DNA. The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment.
format	article
author	Jonas Ghyselinck Stefan Pfeiffer Kim Heylen Angela Sessitsch Paul De Vos
author_facet	Jonas Ghyselinck Stefan Pfeiffer Kim Heylen Angela Sessitsch Paul De Vos
author_sort	Jonas Ghyselinck
title	The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
title_short	The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
title_full	The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
title_fullStr	The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
title_full_unstemmed	The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
title_sort	effect of primer choice and short read sequences on the outcome of 16s rrna gene based diversity studies.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/ea3b8b9b92254950b771d94543b9bc2a
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The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.

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