Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease

Detalhes bibliográficos
Autor(a) principal: Carvalho, Vanessa Rafaela de [UNESP]
Data de Publicação: 2016
Outros Autores: Keller, Rogeria [UNESP], Silva Santos, Ana Carolina da [UNESP], Rodrigues, Josias [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.4236/aim.2016.68055
http://hdl.handle.net/11449/163110
Resumo: Escherichia coli and other Proteobacteria are augmented and several other bacteria are diminished in Crohn's (CD) disease patients' intestine. This imbalance in bacterial species composition-termed dysbiosis-seems to be determinant of CD manifestation. Since a great part of intestinal bacteria are not cultivable, detection of CD dysbiosis is accomplished by molecular tools, involving sequences analysis of the 16SrRNA gene (16SrDNA) present in the patient's clinical samples, which can be done by sequencing or electrophoresis in denaturing gels of 16SrDNA amplicons. By analyzing, by temperature gradient gel electrophoresis (TGGE) and next generation sequencing of 16SV6-V8rDNA amplicons present in gram negative cultures from four distinct clinical samples of a control subject and a CD patient, this study demonstrates that both techniques were able to detect E. coli over-growth and reduction in species richness in CD and that TGGE can discriminate sequences collectively labeled as unclassified in 16SrDNA databases. Although TGGE per se does not identify the sequences, the discriminatory power that it confers represents valuable accessory information to next generation DNA sequencing (NGS), and as such must be used as a NGS complementary tool.
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spelling Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's DiseaseDysbiosisProteobacteriaEscherichia coliCrohn's DiseaseEscherichia coli and other Proteobacteria are augmented and several other bacteria are diminished in Crohn's (CD) disease patients' intestine. This imbalance in bacterial species composition-termed dysbiosis-seems to be determinant of CD manifestation. Since a great part of intestinal bacteria are not cultivable, detection of CD dysbiosis is accomplished by molecular tools, involving sequences analysis of the 16SrRNA gene (16SrDNA) present in the patient's clinical samples, which can be done by sequencing or electrophoresis in denaturing gels of 16SrDNA amplicons. By analyzing, by temperature gradient gel electrophoresis (TGGE) and next generation sequencing of 16SV6-V8rDNA amplicons present in gram negative cultures from four distinct clinical samples of a control subject and a CD patient, this study demonstrates that both techniques were able to detect E. coli over-growth and reduction in species richness in CD and that TGGE can discriminate sequences collectively labeled as unclassified in 16SrDNA databases. Although TGGE per se does not identify the sequences, the discriminatory power that it confers represents valuable accessory information to next generation DNA sequencing (NGS), and as such must be used as a NGS complementary tool.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)State Univ Sao Paulo, UNESP, Lab Med Bacteriol, Dept Microbiol & Immunol,Inst Biosci, Botucatu, SP, BrazilUniv Western Sao Paulo, Presidente Prudente, BrazilState Univ Sao Paulo, UNESP, Lab Med Bacteriol, Dept Microbiol & Immunol,Inst Biosci, Botucatu, SP, BrazilFAPESP: 2013/04475-3Hans PublishersUniversidade Estadual Paulista (Unesp)Univ Western Sao PauloCarvalho, Vanessa Rafaela de [UNESP]Keller, Rogeria [UNESP]Silva Santos, Ana Carolina da [UNESP]Rodrigues, Josias [UNESP]2018-11-26T17:40:09Z2018-11-26T17:40:09Z2016-07-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article549-554application/pdfhttp://dx.doi.org/10.4236/aim.2016.68055Advances In Microbiology. Irvine: Hans Publishers, v. 6, n. 8, p. 549-554, 2016.2327-0810http://hdl.handle.net/11449/16311010.4236/aim.2016.68055WOS:000407163300001WOS000407163300001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengAdvances In Microbiologyinfo:eu-repo/semantics/openAccess2023-10-24T06:11:23Zoai:repositorio.unesp.br:11449/163110Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T15:50:28.917777Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
title Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
spellingShingle Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
Carvalho, Vanessa Rafaela de [UNESP]
Dysbiosis
Proteobacteria
Escherichia coli
Crohn's Disease
title_short Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
title_full Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
title_fullStr Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
title_full_unstemmed Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
title_sort Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn's Disease
author Carvalho, Vanessa Rafaela de [UNESP]
author_facet Carvalho, Vanessa Rafaela de [UNESP]
Keller, Rogeria [UNESP]
Silva Santos, Ana Carolina da [UNESP]
Rodrigues, Josias [UNESP]
author_role author
author2 Keller, Rogeria [UNESP]
Silva Santos, Ana Carolina da [UNESP]
Rodrigues, Josias [UNESP]
author2_role author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Univ Western Sao Paulo
dc.contributor.author.fl_str_mv Carvalho, Vanessa Rafaela de [UNESP]
Keller, Rogeria [UNESP]
Silva Santos, Ana Carolina da [UNESP]
Rodrigues, Josias [UNESP]
dc.subject.por.fl_str_mv Dysbiosis
Proteobacteria
Escherichia coli
Crohn's Disease
topic Dysbiosis
Proteobacteria
Escherichia coli
Crohn's Disease
description Escherichia coli and other Proteobacteria are augmented and several other bacteria are diminished in Crohn's (CD) disease patients' intestine. This imbalance in bacterial species composition-termed dysbiosis-seems to be determinant of CD manifestation. Since a great part of intestinal bacteria are not cultivable, detection of CD dysbiosis is accomplished by molecular tools, involving sequences analysis of the 16SrRNA gene (16SrDNA) present in the patient's clinical samples, which can be done by sequencing or electrophoresis in denaturing gels of 16SrDNA amplicons. By analyzing, by temperature gradient gel electrophoresis (TGGE) and next generation sequencing of 16SV6-V8rDNA amplicons present in gram negative cultures from four distinct clinical samples of a control subject and a CD patient, this study demonstrates that both techniques were able to detect E. coli over-growth and reduction in species richness in CD and that TGGE can discriminate sequences collectively labeled as unclassified in 16SrDNA databases. Although TGGE per se does not identify the sequences, the discriminatory power that it confers represents valuable accessory information to next generation DNA sequencing (NGS), and as such must be used as a NGS complementary tool.
publishDate 2016
dc.date.none.fl_str_mv 2016-07-01
2018-11-26T17:40:09Z
2018-11-26T17:40:09Z
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 http://dx.doi.org/10.4236/aim.2016.68055
Advances In Microbiology. Irvine: Hans Publishers, v. 6, n. 8, p. 549-554, 2016.
2327-0810
http://hdl.handle.net/11449/163110
10.4236/aim.2016.68055
WOS:000407163300001
WOS000407163300001.pdf
url http://dx.doi.org/10.4236/aim.2016.68055
http://hdl.handle.net/11449/163110
identifier_str_mv Advances In Microbiology. Irvine: Hans Publishers, v. 6, n. 8, p. 549-554, 2016.
2327-0810
10.4236/aim.2016.68055
WOS:000407163300001
WOS000407163300001.pdf
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Advances In Microbiology
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 549-554
application/pdf
dc.publisher.none.fl_str_mv Hans Publishers
publisher.none.fl_str_mv Hans Publishers
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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