Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases

Detalhes bibliográficos
Autor(a) principal: Pylro, Victor Satler
Data de Publicação: 2016
Outros Autores: Morais, Daniel Kumazawa, Kalks, Karlos Henrique Martins, Roesch, Luiz Fernando Wurdig, Hirsch, Penny R., Tótola, Marcos Rogério, Yotoko, Karla
Tipo de documento: Artigo
Idioma: eng
Título da fonte: LOCUS Repositório Institucional da UFV
Texto Completo: https://doi.org/10.1016/j.mimet.2016.04.012
http://www.locus.ufv.br/handle/123456789/19237
Resumo: Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.
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spelling Pylro, Victor SatlerMorais, Daniel KumazawaKalks, Karlos Henrique MartinsRoesch, Luiz Fernando WurdigHirsch, Penny R.Tótola, Marcos RogérioYotoko, Karla2018-05-02T13:21:29Z2018-05-02T13:21:29Z2016-04-2201677012https://doi.org/10.1016/j.mimet.2016.04.012http://www.locus.ufv.br/handle/123456789/19237Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.engJournal of Microbiological Methodsv. 126, p. 18-23, July 2016Elsevier B.V.info:eu-repo/semantics/openAccess16S rRNA genePCR-DGGE bacteria phylogenyPublic databasesMisguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databasesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALartigo.pdfartigo.pdfTexto completoapplication/pdf413058https://locus.ufv.br//bitstream/123456789/19237/1/artigo.pdf9ef3ae7d36b6db265afe718de38be1c1MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://locus.ufv.br//bitstream/123456789/19237/2/license.txt8a4605be74aa9ea9d79846c1fba20a33MD52THUMBNAILartigo.pdf.jpgartigo.pdf.jpgIM Thumbnailimage/jpeg5977https://locus.ufv.br//bitstream/123456789/19237/3/artigo.pdf.jpgc14236eb0df8d3a7712292d092f1cecdMD53123456789/192372018-05-02 23:00:44.573oai:locus.ufv.br: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Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452018-05-03T02:00:44LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false
dc.title.en.fl_str_mv Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
title Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
spellingShingle Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
Pylro, Victor Satler
16S rRNA gene
PCR-DGGE bacteria phylogeny
Public databases
title_short Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
title_full Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
title_fullStr Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
title_full_unstemmed Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
title_sort Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases
author Pylro, Victor Satler
author_facet Pylro, Victor Satler
Morais, Daniel Kumazawa
Kalks, Karlos Henrique Martins
Roesch, Luiz Fernando Wurdig
Hirsch, Penny R.
Tótola, Marcos Rogério
Yotoko, Karla
author_role author
author2 Morais, Daniel Kumazawa
Kalks, Karlos Henrique Martins
Roesch, Luiz Fernando Wurdig
Hirsch, Penny R.
Tótola, Marcos Rogério
Yotoko, Karla
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Pylro, Victor Satler
Morais, Daniel Kumazawa
Kalks, Karlos Henrique Martins
Roesch, Luiz Fernando Wurdig
Hirsch, Penny R.
Tótola, Marcos Rogério
Yotoko, Karla
dc.subject.pt-BR.fl_str_mv 16S rRNA gene
PCR-DGGE bacteria phylogeny
Public databases
topic 16S rRNA gene
PCR-DGGE bacteria phylogeny
Public databases
description Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.
publishDate 2016
dc.date.issued.fl_str_mv 2016-04-22
dc.date.accessioned.fl_str_mv 2018-05-02T13:21:29Z
dc.date.available.fl_str_mv 2018-05-02T13:21:29Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv https://doi.org/10.1016/j.mimet.2016.04.012
http://www.locus.ufv.br/handle/123456789/19237
dc.identifier.issn.none.fl_str_mv 01677012
identifier_str_mv 01677012
url https://doi.org/10.1016/j.mimet.2016.04.012
http://www.locus.ufv.br/handle/123456789/19237
dc.language.iso.fl_str_mv eng
language eng
dc.relation.ispartofseries.pt-BR.fl_str_mv v. 126, p. 18-23, July 2016
dc.rights.driver.fl_str_mv Elsevier B.V.
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Elsevier B.V.
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Journal of Microbiological Methods
publisher.none.fl_str_mv Journal of Microbiological Methods
dc.source.none.fl_str_mv reponame:LOCUS Repositório Institucional da UFV
instname:Universidade Federal de Viçosa (UFV)
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instacron_str UFV
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reponame_str LOCUS Repositório Institucional da UFV
collection LOCUS Repositório Institucional da UFV
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