The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Brazilian Journal of Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100242 |
Resumo: | Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates. |
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Brazilian Journal of Biology |
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|
spelling |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCRArchaeaPCRuniversal primersenvironmental microbiologyAbstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.Instituto Internacional de Ecologia2023-01-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100242Brazilian Journal of Biology v.83 2023reponame:Brazilian Journal of Biologyinstname:Instituto Internacional de Ecologia (IIE)instacron:IIE10.1590/1519-6984.247529info:eu-repo/semantics/openAccessBelmok,A.Rodrigues-Oliveira,T.Lopes,F.A.C.Krüger,R.H.Kyaw,C.M.eng2021-09-10T00:00:00Zoai:scielo:S1519-69842023000100242Revistahttps://www.scielo.br/j/bjb/https://old.scielo.br/oai/scielo-oai.phpbjb@bjb.com.br||bjb@bjb.com.br1678-43751519-6984opendoar:2021-09-10T00:00Brazilian Journal of Biology - Instituto Internacional de Ecologia (IIE)false |
dc.title.none.fl_str_mv |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
title |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
spellingShingle |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR Belmok,A. Archaea PCR universal primers environmental microbiology |
title_short |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
title_full |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
title_fullStr |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
title_full_unstemmed |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
title_sort |
The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR |
author |
Belmok,A. |
author_facet |
Belmok,A. Rodrigues-Oliveira,T. Lopes,F.A.C. Krüger,R.H. Kyaw,C.M. |
author_role |
author |
author2 |
Rodrigues-Oliveira,T. Lopes,F.A.C. Krüger,R.H. Kyaw,C.M. |
author2_role |
author author author author |
dc.contributor.author.fl_str_mv |
Belmok,A. Rodrigues-Oliveira,T. Lopes,F.A.C. Krüger,R.H. Kyaw,C.M. |
dc.subject.por.fl_str_mv |
Archaea PCR universal primers environmental microbiology |
topic |
Archaea PCR universal primers environmental microbiology |
description |
Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-01-01 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100242 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842023000100242 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/1519-6984.247529 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/html |
dc.publisher.none.fl_str_mv |
Instituto Internacional de Ecologia |
publisher.none.fl_str_mv |
Instituto Internacional de Ecologia |
dc.source.none.fl_str_mv |
Brazilian Journal of Biology v.83 2023 reponame:Brazilian Journal of Biology instname:Instituto Internacional de Ecologia (IIE) instacron:IIE |
instname_str |
Instituto Internacional de Ecologia (IIE) |
instacron_str |
IIE |
institution |
IIE |
reponame_str |
Brazilian Journal of Biology |
collection |
Brazilian Journal of Biology |
repository.name.fl_str_mv |
Brazilian Journal of Biology - Instituto Internacional de Ecologia (IIE) |
repository.mail.fl_str_mv |
bjb@bjb.com.br||bjb@bjb.com.br |
_version_ |
1752129890221555712 |