Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano
Ano de defesa: | 2013 |
---|---|
Autor(a) principal: | |
Orientador(a): | |
Banca de defesa: | |
Tipo de documento: | Dissertação |
Tipo de acesso: | Acesso aberto |
Idioma: | por |
Instituição de defesa: |
Universidade Católica de Brasília
|
Programa de Pós-Graduação: |
Programa Stricto Sensu em Ciências Genômicas e Biotecnologia
|
Departamento: |
Escola de Saúde e Medicina
|
País: |
Brasil
|
Palavras-chave em Português: | |
Palavras-chave em Inglês: | |
Área do conhecimento CNPq: | |
Resumo em Inglês: | Humans live in constant association with microorganims. The amount of microorganims present in the human body exceeds our own cell number. That community of microorganisms has deep influence in health and disease. The use of high-throughput DNA sequencing technologies and culture independent approaches have been enlarging the understanding concerning the communities of microorganisms and the association of these with the host. The human gastrointestinal tract contains one of the most complex bacterial communities. It was proposed recently that the microbiome can be classified in three enterotypes. In our study, we used data metagenomics quantitative search to identify phylogenetic patterns in the intestinal microbiome to develop prediction models for the enterotypes. To reach this aim, statistical tests were applied to the data regarding abundance of bacteria in level taxonomic corresponding to genus. We identified genus significantly with the abundance different and important correlations. Besides the ratio among genus to be used as parameter bioindicator of the respectives enterotypes. Through the logistic regression test we identified that the prediction model for ET1 was influenced significantly by the ratio of Bacteroides / (Prevotella + Ruminococcus). In the model for prediction of ET2, it was the ratio of Prevotella / Bacteroides with such as characteristic significance. And for the model of ET3, we identified the ratio of (Akkermansia + Alistipes) / (Bacteroides + Prevotella) as significant parameter. These models were assessed against two groups of independent data and associated with the value of cut-off 5%; 20% and 95% respectively. Besides the value of cutoff for each models, the crossed validation allowed the association of the model with the measures of PPV for ET1, specificity for ET2 and PNV for ET3. We propose the experimental validation of these models for the qPCR technique. And with that methodology established, it would be possible to do the diagnosis of the enterotype individually. |
Link de acesso: | https://bdtd.ucb.br:8443/jspui/handle/tede/2473 |
Resumo: | Humans live in constant association with microorganims. The amount of microorganims present in the human body exceeds our own cell number. That community of microorganisms has deep influence in health and disease. The use of high-throughput DNA sequencing technologies and culture independent approaches have been enlarging the understanding concerning the communities of microorganisms and the association of these with the host. The human gastrointestinal tract contains one of the most complex bacterial communities. It was proposed recently that the microbiome can be classified in three enterotypes. In our study, we used data metagenomics quantitative search to identify phylogenetic patterns in the intestinal microbiome to develop prediction models for the enterotypes. To reach this aim, statistical tests were applied to the data regarding abundance of bacteria in level taxonomic corresponding to genus. We identified genus significantly with the abundance different and important correlations. Besides the ratio among genus to be used as parameter bioindicator of the respectives enterotypes. Through the logistic regression test we identified that the prediction model for ET1 was influenced significantly by the ratio of Bacteroides / (Prevotella + Ruminococcus). In the model for prediction of ET2, it was the ratio of Prevotella / Bacteroides with such as characteristic significance. And for the model of ET3, we identified the ratio of (Akkermansia + Alistipes) / (Bacteroides + Prevotella) as significant parameter. These models were assessed against two groups of independent data and associated with the value of cut-off 5%; 20% and 95% respectively. Besides the value of cutoff for each models, the crossed validation allowed the association of the model with the measures of PPV for ET1, specificity for ET2 and PNV for ET3. We propose the experimental validation of these models for the qPCR technique. And with that methodology established, it would be possible to do the diagnosis of the enterotype individually. |
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Fernandes, Gabriel da Rochahttp://lattes.cnpq.br/8989178759075946Barreto, Cristine Chaveshttp://lattes.cnpq.br/9973148799581550http://lattes.cnpq.br/9425556823276996Veras, Henrique César Teixeira2018-11-07T17:35:09Z2013-09-06VERAS, Henrique César Teixeira. Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano. 2013. 88 f. Dissertação (Programa Stricto Sensu em Ciências Genômicas e Biotecnologia) - Universidade Católica de Brasília, Brasília, 2013.https://bdtd.ucb.br:8443/jspui/handle/tede/2473Humans live in constant association with microorganims. The amount of microorganims present in the human body exceeds our own cell number. That community of microorganisms has deep influence in health and disease. The use of high-throughput DNA sequencing technologies and culture independent approaches have been enlarging the understanding concerning the communities of microorganisms and the association of these with the host. The human gastrointestinal tract contains one of the most complex bacterial communities. It was proposed recently that the microbiome can be classified in three enterotypes. In our study, we used data metagenomics quantitative search to identify phylogenetic patterns in the intestinal microbiome to develop prediction models for the enterotypes. To reach this aim, statistical tests were applied to the data regarding abundance of bacteria in level taxonomic corresponding to genus. We identified genus significantly with the abundance different and important correlations. Besides the ratio among genus to be used as parameter bioindicator of the respectives enterotypes. Through the logistic regression test we identified that the prediction model for ET1 was influenced significantly by the ratio of Bacteroides / (Prevotella + Ruminococcus). In the model for prediction of ET2, it was the ratio of Prevotella / Bacteroides with such as characteristic significance. And for the model of ET3, we identified the ratio of (Akkermansia + Alistipes) / (Bacteroides + Prevotella) as significant parameter. These models were assessed against two groups of independent data and associated with the value of cut-off 5%; 20% and 95% respectively. Besides the value of cutoff for each models, the crossed validation allowed the association of the model with the measures of PPV for ET1, specificity for ET2 and PNV for ET3. We propose the experimental validation of these models for the qPCR technique. And with that methodology established, it would be possible to do the diagnosis of the enterotype individually.Humanos vivem em constante associação com microrganismos. A quantidade de microrganismos presentes no corpo humano ultrapassa o nosso próprio número de células. Essa comunidade de microrganismos tem profunda influência na saúde e doenças. As tecnologias de sequenciamento de DNA de alta capacidade e abordagens moleculares independente de cultura têm ampliado a compreensão acerca das comunidades de microrganismos e a associação destes com o hospedeiro. O trato gastrointestinal humano abriga uma das mais complexas comunidades bacterianas. Foi proposto recentemente que o microbioma pode ser categorizado em três enterotipos. No nosso estudo, utilizamos dados metagenômicos quantitativos buncando identificar padrões filogenéticos no microbioma intestinal para desenvolver modelos de predição para os enterotipos. Para alcançar este objetivo, testes estatísticos foram aplicados aos dados referente a abundância de bactérias em nível taxonômico correspondente a gênero. Identificamos gêneros com a abundância significativamente diferente e correlações importantes. Além da razão entre gêneros para ser utilizada como parâmetro bioindicativo dos respectivos enterotipos. Através do teste de regressão logística identificamos que o modelo de predição para o ET1 foi influenciado significativamente pela razão de Bacteroides / (Prevotella + Ruminococcus). No modelo para predição do ET2, foi a razão de Prevotella / Bacteroides que apresentou significância. E para o modelo do ET3, identificamos a razão de (Akkermansia + Alistipes) / (Bacteroides + Prevotella) como parâmetro significativo. Estes modelos foram avaliados contra dois conjuntos de dados independentes e associados com o valor de cut-off 5%; 20% e; 95% respectivamente. Além do valor de cut-off para cada modelos, a validação cruzada permitiu a associação do modelo com as medidas de PPV para o ET1, especificidade para o ET2 e PNV para o ET3. Propomos a validação experimental destes modelos pela técnica de qPCR. E com essa metodologia estabelecida, seria possível fazer o diagnóstico do enterotipo individualmente.Submitted by Sara Ribeiro (sara.ribeiro@ucb.br) on 2018-11-07T17:34:33Z No. of bitstreams: 1 HenriqueCesarTeixeiraVerasDissertacao2013.pdf: 26147875 bytes, checksum: 3014f6ec0d791f46e4e1ee8c49894c2f (MD5)Approved for entry into archive by Sara Ribeiro (sara.ribeiro@ucb.br) on 2018-11-07T17:35:09Z (GMT) No. of bitstreams: 1 HenriqueCesarTeixeiraVerasDissertacao2013.pdf: 26147875 bytes, checksum: 3014f6ec0d791f46e4e1ee8c49894c2f (MD5)Made available in DSpace on 2018-11-07T17:35:09Z (GMT). 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dc.title.por.fl_str_mv |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
title |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
spellingShingle |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano Veras, Henrique César Teixeira Enterotipos Bioindicadores Metagenômica Microbiota intestinal Gut microbiota Metagenomics Bioindicators Enterotypes CNPQ::CIENCIAS BIOLOGICAS |
title_short |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
title_full |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
title_fullStr |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
title_full_unstemmed |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
title_sort |
Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano |
author |
Veras, Henrique César Teixeira |
author_facet |
Veras, Henrique César Teixeira |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Fernandes, Gabriel da Rocha |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/8989178759075946 |
dc.contributor.advisor-co1.fl_str_mv |
Barreto, Cristine Chaves |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://lattes.cnpq.br/9973148799581550 |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/9425556823276996 |
dc.contributor.author.fl_str_mv |
Veras, Henrique César Teixeira |
contributor_str_mv |
Fernandes, Gabriel da Rocha Barreto, Cristine Chaves |
dc.subject.por.fl_str_mv |
Enterotipos Bioindicadores Metagenômica Microbiota intestinal |
topic |
Enterotipos Bioindicadores Metagenômica Microbiota intestinal Gut microbiota Metagenomics Bioindicators Enterotypes CNPQ::CIENCIAS BIOLOGICAS |
dc.subject.eng.fl_str_mv |
Gut microbiota Metagenomics Bioindicators Enterotypes |
dc.subject.cnpq.fl_str_mv |
CNPQ::CIENCIAS BIOLOGICAS |
dc.description.abstract.eng.fl_txt_mv |
Humans live in constant association with microorganims. The amount of microorganims present in the human body exceeds our own cell number. That community of microorganisms has deep influence in health and disease. The use of high-throughput DNA sequencing technologies and culture independent approaches have been enlarging the understanding concerning the communities of microorganisms and the association of these with the host. The human gastrointestinal tract contains one of the most complex bacterial communities. It was proposed recently that the microbiome can be classified in three enterotypes. In our study, we used data metagenomics quantitative search to identify phylogenetic patterns in the intestinal microbiome to develop prediction models for the enterotypes. To reach this aim, statistical tests were applied to the data regarding abundance of bacteria in level taxonomic corresponding to genus. We identified genus significantly with the abundance different and important correlations. Besides the ratio among genus to be used as parameter bioindicator of the respectives enterotypes. Through the logistic regression test we identified that the prediction model for ET1 was influenced significantly by the ratio of Bacteroides / (Prevotella + Ruminococcus). In the model for prediction of ET2, it was the ratio of Prevotella / Bacteroides with such as characteristic significance. And for the model of ET3, we identified the ratio of (Akkermansia + Alistipes) / (Bacteroides + Prevotella) as significant parameter. These models were assessed against two groups of independent data and associated with the value of cut-off 5%; 20% and 95% respectively. Besides the value of cutoff for each models, the crossed validation allowed the association of the model with the measures of PPV for ET1, specificity for ET2 and PNV for ET3. We propose the experimental validation of these models for the qPCR technique. And with that methodology established, it would be possible to do the diagnosis of the enterotype individually. |
dc.description.abstract.por.fl_txt_mv |
Humanos vivem em constante associação com microrganismos. A quantidade de microrganismos presentes no corpo humano ultrapassa o nosso próprio número de células. Essa comunidade de microrganismos tem profunda influência na saúde e doenças. As tecnologias de sequenciamento de DNA de alta capacidade e abordagens moleculares independente de cultura têm ampliado a compreensão acerca das comunidades de microrganismos e a associação destes com o hospedeiro. O trato gastrointestinal humano abriga uma das mais complexas comunidades bacterianas. Foi proposto recentemente que o microbioma pode ser categorizado em três enterotipos. No nosso estudo, utilizamos dados metagenômicos quantitativos buncando identificar padrões filogenéticos no microbioma intestinal para desenvolver modelos de predição para os enterotipos. Para alcançar este objetivo, testes estatísticos foram aplicados aos dados referente a abundância de bactérias em nível taxonômico correspondente a gênero. Identificamos gêneros com a abundância significativamente diferente e correlações importantes. Além da razão entre gêneros para ser utilizada como parâmetro bioindicativo dos respectivos enterotipos. Através do teste de regressão logística identificamos que o modelo de predição para o ET1 foi influenciado significativamente pela razão de Bacteroides / (Prevotella + Ruminococcus). No modelo para predição do ET2, foi a razão de Prevotella / Bacteroides que apresentou significância. E para o modelo do ET3, identificamos a razão de (Akkermansia + Alistipes) / (Bacteroides + Prevotella) como parâmetro significativo. Estes modelos foram avaliados contra dois conjuntos de dados independentes e associados com o valor de cut-off 5%; 20% e; 95% respectivamente. Além do valor de cut-off para cada modelos, a validação cruzada permitiu a associação do modelo com as medidas de PPV para o ET1, especificidade para o ET2 e PNV para o ET3. Propomos a validação experimental destes modelos pela técnica de qPCR. E com essa metodologia estabelecida, seria possível fazer o diagnóstico do enterotipo individualmente. |
description |
Humans live in constant association with microorganims. The amount of microorganims present in the human body exceeds our own cell number. That community of microorganisms has deep influence in health and disease. The use of high-throughput DNA sequencing technologies and culture independent approaches have been enlarging the understanding concerning the communities of microorganisms and the association of these with the host. The human gastrointestinal tract contains one of the most complex bacterial communities. It was proposed recently that the microbiome can be classified in three enterotypes. In our study, we used data metagenomics quantitative search to identify phylogenetic patterns in the intestinal microbiome to develop prediction models for the enterotypes. To reach this aim, statistical tests were applied to the data regarding abundance of bacteria in level taxonomic corresponding to genus. We identified genus significantly with the abundance different and important correlations. Besides the ratio among genus to be used as parameter bioindicator of the respectives enterotypes. Through the logistic regression test we identified that the prediction model for ET1 was influenced significantly by the ratio of Bacteroides / (Prevotella + Ruminococcus). In the model for prediction of ET2, it was the ratio of Prevotella / Bacteroides with such as characteristic significance. And for the model of ET3, we identified the ratio of (Akkermansia + Alistipes) / (Bacteroides + Prevotella) as significant parameter. These models were assessed against two groups of independent data and associated with the value of cut-off 5%; 20% and 95% respectively. Besides the value of cutoff for each models, the crossed validation allowed the association of the model with the measures of PPV for ET1, specificity for ET2 and PNV for ET3. We propose the experimental validation of these models for the qPCR technique. And with that methodology established, it would be possible to do the diagnosis of the enterotype individually. |
publishDate |
2013 |
dc.date.issued.fl_str_mv |
2013-09-06 |
dc.date.accessioned.fl_str_mv |
2018-11-07T17:35:09Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
status_str |
publishedVersion |
format |
masterThesis |
dc.identifier.citation.fl_str_mv |
VERAS, Henrique César Teixeira. Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano. 2013. 88 f. Dissertação (Programa Stricto Sensu em Ciências Genômicas e Biotecnologia) - Universidade Católica de Brasília, Brasília, 2013. |
dc.identifier.uri.fl_str_mv |
https://bdtd.ucb.br:8443/jspui/handle/tede/2473 |
identifier_str_mv |
VERAS, Henrique César Teixeira. Bioindicadores filogenéticos para predição dos enterotipos do microbioma intestinal humano. 2013. 88 f. Dissertação (Programa Stricto Sensu em Ciências Genômicas e Biotecnologia) - Universidade Católica de Brasília, Brasília, 2013. |
url |
https://bdtd.ucb.br:8443/jspui/handle/tede/2473 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Católica de Brasília |
dc.publisher.program.fl_str_mv |
Programa Stricto Sensu em Ciências Genômicas e Biotecnologia |
dc.publisher.initials.fl_str_mv |
UCB |
dc.publisher.country.fl_str_mv |
Brasil |
dc.publisher.department.fl_str_mv |
Escola de Saúde e Medicina |
publisher.none.fl_str_mv |
Universidade Católica de Brasília |
dc.source.none.fl_str_mv |
reponame:Biblioteca Digital de Teses e Dissertações da UCB instname:Universidade Católica de Brasília instacron:UCB |
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Biblioteca Digital de Teses e Dissertações da UCB |
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Universidade Católica de Brasília |
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UCB |
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bitstream.checksum.fl_str_mv |
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MD5 MD5 MD5 MD5 |
repository.name.fl_str_mv |
Biblioteca Digital de Dissertações da Universidade Católica de Brasília - UCB |
repository.mail.fl_str_mv |
sdi@ucb.br |
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1643299889820467200 |