Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Tipo de documento: | Dissertação |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFMG |
Texto Completo: | http://hdl.handle.net/1843/38128 |
Resumo: | Probiotics are microorganisms with the ability to influence the composition of the intestinal microbiota and promote human health. The role of microorganisms in the human microbiota and on health has increased in importance in the last years and more approaches are used to elucidate their properties. Genomics and the bioinformatic analysis of available bacterial data have been used in the main genera of probiotics Lactobacillus e Bifidobacterium. Bifidobacterium breve is considered a safe species, dominant in newborns and it is used in probiotic products. B. breve to treat necrotizing enterocolitis (NEC), gastrointestinal disorders, celiac disease, pediatric obesity, and allergies in infants with positive results. In this context, the present study aims to perform the in silico characterization of the genome of Bifidobacterium breve 1101A strain through a comparative genomic analysis and the identification of genes related to probiotic features. For this purpose, it was employed additional 45 available complete genomes of Bifidobacterium breve to (i) analyze the taxonomic and phylogenomic aspects of this genus, (ii) identify mobile elements in the 1101A genome such as prophages, plasmids, IS, (iii) genomic islands (GEI), antibiotic resistance genes and (iv) analyze the pangenome. Between the results, the strain 1101A was identified as Bifidobacterium breve and the phylogenetically closest strain was B. breve NRBB26. An incomplete prophage was predicted in B. breve 1101A genome, without plasmids. Moreover, seven genomic islands (GEI) were identified: two Resistance Islands (RI) and five Genomic Islands (GI). Resistance genes present in the genome were rpoB, iles and ermX. The pangenome size was calculated in 5943 genes and the core genome in 1174 genes and it was considered an open pangenome according to previous studies. There were 63 unique genes related to the metabolism of carbohydrates, such as galactosidase and DNA binding. Also, some genes related to adherence, resistance to stress, repair and protection of DNA and proteins, production of vitamins was identified. These results reveal the probiotic potential of this bacterial strain and direct further studies in vitro and in vivo to confirm its properties. |
id |
UFMG_0c2c97a47b9a84bf09125f8bcfaf1e04 |
---|---|
oai_identifier_str |
oai:repositorio.ufmg.br:1843/38128 |
network_acronym_str |
UFMG |
network_name_str |
Repositório Institucional da UFMG |
repository_id_str |
|
spelling |
Vasco Ariston de Carvalho Azevedohttp://lattes.cnpq.br/1020477751003832Flavia Figueira AburjaileSiomar de Castro SoaresRommel Thiago Juca RamosRonnie Gustavo Gavilan Chavezhttp://lattes.cnpq.br/2350650408681552Juan Luis Valdez Baez2021-09-22T12:57:34Z2021-09-22T12:57:34Z2021-05-31http://hdl.handle.net/1843/38128Probiotics are microorganisms with the ability to influence the composition of the intestinal microbiota and promote human health. The role of microorganisms in the human microbiota and on health has increased in importance in the last years and more approaches are used to elucidate their properties. Genomics and the bioinformatic analysis of available bacterial data have been used in the main genera of probiotics Lactobacillus e Bifidobacterium. Bifidobacterium breve is considered a safe species, dominant in newborns and it is used in probiotic products. B. breve to treat necrotizing enterocolitis (NEC), gastrointestinal disorders, celiac disease, pediatric obesity, and allergies in infants with positive results. In this context, the present study aims to perform the in silico characterization of the genome of Bifidobacterium breve 1101A strain through a comparative genomic analysis and the identification of genes related to probiotic features. For this purpose, it was employed additional 45 available complete genomes of Bifidobacterium breve to (i) analyze the taxonomic and phylogenomic aspects of this genus, (ii) identify mobile elements in the 1101A genome such as prophages, plasmids, IS, (iii) genomic islands (GEI), antibiotic resistance genes and (iv) analyze the pangenome. Between the results, the strain 1101A was identified as Bifidobacterium breve and the phylogenetically closest strain was B. breve NRBB26. An incomplete prophage was predicted in B. breve 1101A genome, without plasmids. Moreover, seven genomic islands (GEI) were identified: two Resistance Islands (RI) and five Genomic Islands (GI). Resistance genes present in the genome were rpoB, iles and ermX. The pangenome size was calculated in 5943 genes and the core genome in 1174 genes and it was considered an open pangenome according to previous studies. There were 63 unique genes related to the metabolism of carbohydrates, such as galactosidase and DNA binding. Also, some genes related to adherence, resistance to stress, repair and protection of DNA and proteins, production of vitamins was identified. These results reveal the probiotic potential of this bacterial strain and direct further studies in vitro and in vivo to confirm its properties.Os probióticos são microrganismos com capacidade de influenciar na composição da microbiota intestinal, devido aos seus efeitos benéficos aos hospedeiros que nos levam a explorar mecanismos de ação através de estudos in silico e experimentais. O papel dos microrganismos na microbiota humana e na saúde têm aumentado em importância nos últimos anos e mais abordagens são utilizadas para elucidar suas propriedades. A genômica por meio da análise bioinformática de dados bacterianos disponíveis tem sido usada nos principais gêneros de probióticos Lactobacillus e Bifidobacterium. Bifidobacterium breve é considerada uma espécie secura, dominante em recém-nascidos e é usado em produtos probióticos. B. breve tem sido usado no tratamento de enterocolites necrosante (NEC), desordens gastrointestinais, doenças celíacas, obesidade pediátrica e alergias em infantes com efeitos positivos. Nesse contexto, o objetivo do presente estudo é a caracterizar in silico do genoma de Bifidobacterium breve 1101A por meio de análises comparativas, visando a busca de genes relacionados ao potencial probiótico. Para isso, foram empregados adicionalmente 45 genomas completos disponíveis de B. breve para (i) analisar aspectos taxonômicos e filogenômicos de este género, (ii) identificação de elementos móveis no genoma 1101A como profagos, plasmídeos, IS, (iii) ilhas genômicas e (iv) análise de pangenoma. Os resultados da filogenômica demonstram que a nossa linhagem em estudo, B. breve 1101A, foi clusterizada mais próxima de B. breve NRBB26. B. breve 1101A apresentou um profago incompleto e nenhum plasmídeo. Além disso, sete ilhas genômicas (GEI) foram identificadas, sendo duas ilhas de resistência (RI) e cinco ilhas genômicas (GI). O pangenoma possui 5943 genes e o genoma central 1174 genes, sendo considerado como um pangenoma aberto, de acordo com estudos anteriores. Foram identificados 63 genes únicos, alguns deles relacionados ao metabolismo de carboidratos, como galactosidase, e ligação ao DNA. Também foram identificados alguns genes relacionados a aderência, resistência ao estresse, reparo e proteção de DNA e proteínas, produção de vitaminas. Estes resultados revelam o potencial probiótico desta linhagem bacteriana e direcionam á estudos in vitro e in vivo para confirmar suas propriedades.FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas GeraisCAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorengUniversidade Federal de Minas GeraisPrograma de Pós-Graduação em BioinformaticaUFMGBrasilICB - INSTITUTO DE CIÊNCIAS BIOLOGICASBiologia computacionalGenômicaProbióticosBifidobacteriumPangenomic analysesComparative genomicsProbioticBifidobacterium breveComparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101ainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFMGinstname:Universidade Federal de Minas Gerais (UFMG)instacron:UFMGORIGINALDissertation_Juan_Valdez.pdfDissertation_Juan_Valdez.pdfapplication/pdf3953127https://repositorio.ufmg.br/bitstream/1843/38128/1/Dissertation_Juan_Valdez.pdf61acb42cfa4cad5616158908531bdfcfMD51LICENSElicense.txtlicense.txttext/plain; charset=utf-82118https://repositorio.ufmg.br/bitstream/1843/38128/2/license.txtcda590c95a0b51b4d15f60c9642ca272MD521843/381282023-02-09 16:26:57.092oai:repositorio.ufmg.br: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ório de PublicaçõesPUBhttps://repositorio.ufmg.br/oaiopendoar:2023-02-09T19:26:57Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG)false |
dc.title.pt_BR.fl_str_mv |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
title |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
spellingShingle |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a Juan Luis Valdez Baez Pangenomic analyses Comparative genomics Probiotic Bifidobacterium breve Biologia computacional Genômica Probióticos Bifidobacterium |
title_short |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
title_full |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
title_fullStr |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
title_full_unstemmed |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
title_sort |
Comparative genomics and in silico evaluation of genes related to probiotic potential of Bifidobacterium breve 1101a |
author |
Juan Luis Valdez Baez |
author_facet |
Juan Luis Valdez Baez |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Vasco Ariston de Carvalho Azevedo |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/1020477751003832 |
dc.contributor.advisor-co1.fl_str_mv |
Flavia Figueira Aburjaile |
dc.contributor.referee1.fl_str_mv |
Siomar de Castro Soares |
dc.contributor.referee2.fl_str_mv |
Rommel Thiago Juca Ramos |
dc.contributor.referee3.fl_str_mv |
Ronnie Gustavo Gavilan Chavez |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/2350650408681552 |
dc.contributor.author.fl_str_mv |
Juan Luis Valdez Baez |
contributor_str_mv |
Vasco Ariston de Carvalho Azevedo Flavia Figueira Aburjaile Siomar de Castro Soares Rommel Thiago Juca Ramos Ronnie Gustavo Gavilan Chavez |
dc.subject.por.fl_str_mv |
Pangenomic analyses Comparative genomics Probiotic Bifidobacterium breve |
topic |
Pangenomic analyses Comparative genomics Probiotic Bifidobacterium breve Biologia computacional Genômica Probióticos Bifidobacterium |
dc.subject.other.pt_BR.fl_str_mv |
Biologia computacional Genômica Probióticos Bifidobacterium |
description |
Probiotics are microorganisms with the ability to influence the composition of the intestinal microbiota and promote human health. The role of microorganisms in the human microbiota and on health has increased in importance in the last years and more approaches are used to elucidate their properties. Genomics and the bioinformatic analysis of available bacterial data have been used in the main genera of probiotics Lactobacillus e Bifidobacterium. Bifidobacterium breve is considered a safe species, dominant in newborns and it is used in probiotic products. B. breve to treat necrotizing enterocolitis (NEC), gastrointestinal disorders, celiac disease, pediatric obesity, and allergies in infants with positive results. In this context, the present study aims to perform the in silico characterization of the genome of Bifidobacterium breve 1101A strain through a comparative genomic analysis and the identification of genes related to probiotic features. For this purpose, it was employed additional 45 available complete genomes of Bifidobacterium breve to (i) analyze the taxonomic and phylogenomic aspects of this genus, (ii) identify mobile elements in the 1101A genome such as prophages, plasmids, IS, (iii) genomic islands (GEI), antibiotic resistance genes and (iv) analyze the pangenome. Between the results, the strain 1101A was identified as Bifidobacterium breve and the phylogenetically closest strain was B. breve NRBB26. An incomplete prophage was predicted in B. breve 1101A genome, without plasmids. Moreover, seven genomic islands (GEI) were identified: two Resistance Islands (RI) and five Genomic Islands (GI). Resistance genes present in the genome were rpoB, iles and ermX. The pangenome size was calculated in 5943 genes and the core genome in 1174 genes and it was considered an open pangenome according to previous studies. There were 63 unique genes related to the metabolism of carbohydrates, such as galactosidase and DNA binding. Also, some genes related to adherence, resistance to stress, repair and protection of DNA and proteins, production of vitamins was identified. These results reveal the probiotic potential of this bacterial strain and direct further studies in vitro and in vivo to confirm its properties. |
publishDate |
2021 |
dc.date.accessioned.fl_str_mv |
2021-09-22T12:57:34Z |
dc.date.available.fl_str_mv |
2021-09-22T12:57:34Z |
dc.date.issued.fl_str_mv |
2021-05-31 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1843/38128 |
url |
http://hdl.handle.net/1843/38128 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Universidade Federal de Minas Gerais |
dc.publisher.program.fl_str_mv |
Programa de Pós-Graduação em Bioinformatica |
dc.publisher.initials.fl_str_mv |
UFMG |
dc.publisher.country.fl_str_mv |
Brasil |
dc.publisher.department.fl_str_mv |
ICB - INSTITUTO DE CIÊNCIAS BIOLOGICAS |
publisher.none.fl_str_mv |
Universidade Federal de Minas Gerais |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UFMG instname:Universidade Federal de Minas Gerais (UFMG) instacron:UFMG |
instname_str |
Universidade Federal de Minas Gerais (UFMG) |
instacron_str |
UFMG |
institution |
UFMG |
reponame_str |
Repositório Institucional da UFMG |
collection |
Repositório Institucional da UFMG |
bitstream.url.fl_str_mv |
https://repositorio.ufmg.br/bitstream/1843/38128/1/Dissertation_Juan_Valdez.pdf https://repositorio.ufmg.br/bitstream/1843/38128/2/license.txt |
bitstream.checksum.fl_str_mv |
61acb42cfa4cad5616158908531bdfcf cda590c95a0b51b4d15f60c9642ca272 |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG) |
repository.mail.fl_str_mv |
|
_version_ |
1803589275563851776 |