Core of the saliva microbiome: an analysis of the MG-RAST data

Detalhes bibliográficos
Autor(a) principal: Oliveira, Simone G.
Data de Publicação: 2021
Outros Autores: Nishiyama, Rafaela R., Trigo, Claudio A. C., Guaraldi, Ana Luiza Mattos, Dávila, Alberto M. R., Jardim, Rodrigo, Aguiar, Flavio H. B.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/48463
Resumo: Universidade Estadual de Campinas. Escola de Odontologia de Piracicaba. Departamento de Odontologia Restaurativa. Piracicaba, SP, Brasil / Universidade do Estado do Rio de Janeiro. Faculdade de Odontologia. Rio de Janeiro, RJ, Brasil.
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spelling Oliveira, Simone G.Nishiyama, Rafaela R.Trigo, Claudio A. C.Guaraldi, Ana Luiza MattosDávila, Alberto M. R.Jardim, RodrigoAguiar, Flavio H. B.2021-08-01T19:06:57Z2021-08-01T19:06:57Z2021OLIVEIRA, Simone G. et al. Core of the saliva microbiome: an analysis of the MG-RAST data. BMC Oral Health, v. 21, n. 351, 10 p, 2021.1472-6831https://www.arca.fiocruz.br/handle/icict/4846310.1186/s12903-021-01719-5engBMCNúcleo de microbiomaSalivaSequenciamento de ampliconMetagenômica de espingardaMicrobiome coreSalivaMG-RASTAmplicon sequencingShotgun metagenomicseHOMDCore of the saliva microbiome: an analysis of the MG-RAST datainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade Estadual de Campinas. Escola de Odontologia de Piracicaba. Departamento de Odontologia Restaurativa. Piracicaba, SP, Brasil / Universidade do Estado do Rio de Janeiro. Faculdade de Odontologia. Rio de Janeiro, RJ, Brasil.Universidade Estadual de Campinas. Escola de Odontologia de Piracicaba. Departamento de Odontologia Restaurativa. Piracicaba, SP, Brasil.Universidade Estadual de Campinas. Escola de Odontologia de Piracicaba. Departamento de Odontologia Restaurativa. Piracicaba, SP, Brasil.Universidade do Estado do Rio de Janeiro. Faculdade de Ciências Médicas. Laboratório de Difteria e Corynebacteria de Relevância Clínica. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil.Universidade Estadual de Campinas. Escola de Odontologia de Piracicaba. Departamento de Odontologia Restaurativa. Piracicaba, SP, Brasil.Background: Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environ‑ mental behavior from microorganisms. Methods: Projects containing the term “SALIVA”, deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagen‑ omics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann–Whitney U test and Spearman’s correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p<0.05 was used. Results: The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed signifcant diferences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r= −0.78) and the lowest between Alpha and Unknown (r= −0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r=0.63) had the highest correlation and the lowest was between Alpha and Predicted (r= −0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacil lus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter. Conclusions: Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diver‑ sity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identifed 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/48463/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALRodrigoJardim_AlbertoDavila_etal_IOC_2021.pdfRodrigoJardim_AlbertoDavila_etal_IOC_2021.pdfapplication/pdf1861111https://www.arca.fiocruz.br/bitstream/icict/48463/2/RodrigoJardim_AlbertoDavila_etal_IOC_2021.pdfaf873cf74b6f617f8cff6a745e7c0674MD52TEXTRodrigoJardim_AlbertoDavila_etal_IOC_2021.pdf.txtRodrigoJardim_AlbertoDavila_etal_IOC_2021.pdf.txtExtracted texttext/plain38344https://www.arca.fiocruz.br/bitstream/icict/48463/3/RodrigoJardim_AlbertoDavila_etal_IOC_2021.pdf.txt5b7a06b04f9b45d67fc6763ee0180973MD53icict/484632022-06-24 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dc.title.pt_BR.fl_str_mv Core of the saliva microbiome: an analysis of the MG-RAST data
title Core of the saliva microbiome: an analysis of the MG-RAST data
spellingShingle Core of the saliva microbiome: an analysis of the MG-RAST data
Oliveira, Simone G.
Núcleo de microbioma
Saliva
Sequenciamento de amplicon
Metagenômica de espingarda
Microbiome core
Saliva
MG-RAST
Amplicon sequencing
Shotgun metagenomics
eHOMD
title_short Core of the saliva microbiome: an analysis of the MG-RAST data
title_full Core of the saliva microbiome: an analysis of the MG-RAST data
title_fullStr Core of the saliva microbiome: an analysis of the MG-RAST data
title_full_unstemmed Core of the saliva microbiome: an analysis of the MG-RAST data
title_sort Core of the saliva microbiome: an analysis of the MG-RAST data
author Oliveira, Simone G.
author_facet Oliveira, Simone G.
Nishiyama, Rafaela R.
Trigo, Claudio A. C.
Guaraldi, Ana Luiza Mattos
Dávila, Alberto M. R.
Jardim, Rodrigo
Aguiar, Flavio H. B.
author_role author
author2 Nishiyama, Rafaela R.
Trigo, Claudio A. C.
Guaraldi, Ana Luiza Mattos
Dávila, Alberto M. R.
Jardim, Rodrigo
Aguiar, Flavio H. B.
author2_role author
author
author
author
author
author
dc.contributor.author.fl_str_mv Oliveira, Simone G.
Nishiyama, Rafaela R.
Trigo, Claudio A. C.
Guaraldi, Ana Luiza Mattos
Dávila, Alberto M. R.
Jardim, Rodrigo
Aguiar, Flavio H. B.
dc.subject.other.pt_BR.fl_str_mv Núcleo de microbioma
Saliva
Sequenciamento de amplicon
Metagenômica de espingarda
topic Núcleo de microbioma
Saliva
Sequenciamento de amplicon
Metagenômica de espingarda
Microbiome core
Saliva
MG-RAST
Amplicon sequencing
Shotgun metagenomics
eHOMD
dc.subject.en.pt_BR.fl_str_mv Microbiome core
Saliva
MG-RAST
Amplicon sequencing
Shotgun metagenomics
eHOMD
description Universidade Estadual de Campinas. Escola de Odontologia de Piracicaba. Departamento de Odontologia Restaurativa. Piracicaba, SP, Brasil / Universidade do Estado do Rio de Janeiro. Faculdade de Odontologia. Rio de Janeiro, RJ, Brasil.
publishDate 2021
dc.date.accessioned.fl_str_mv 2021-08-01T19:06:57Z
dc.date.available.fl_str_mv 2021-08-01T19:06:57Z
dc.date.issued.fl_str_mv 2021
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.citation.fl_str_mv OLIVEIRA, Simone G. et al. Core of the saliva microbiome: an analysis of the MG-RAST data. BMC Oral Health, v. 21, n. 351, 10 p, 2021.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/48463
dc.identifier.issn.pt_BR.fl_str_mv 1472-6831
dc.identifier.doi.none.fl_str_mv 10.1186/s12903-021-01719-5
identifier_str_mv OLIVEIRA, Simone G. et al. Core of the saliva microbiome: an analysis of the MG-RAST data. BMC Oral Health, v. 21, n. 351, 10 p, 2021.
1472-6831
10.1186/s12903-021-01719-5
url https://www.arca.fiocruz.br/handle/icict/48463
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 BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/48463/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/48463/2/RodrigoJardim_AlbertoDavila_etal_IOC_2021.pdf
https://www.arca.fiocruz.br/bitstream/icict/48463/3/RodrigoJardim_AlbertoDavila_etal_IOC_2021.pdf.txt
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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