Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.

Detalhes bibliográficos
Autor(a) principal: PAZ VENTERO, M.
Data de Publicação: 2021
Outros Autores: CUADRAT, R. R. C., VIDAL, I., ANDRADE, B. G. N., MOLINA-PARDINES, C., HARI-MORENO, J. M., COUTINHO, F. H., MERINO, E., REGITANO, L. C. de A., SILVEIRA, C. B., AFLI, H., LÓPEZ-PÉREZ, M., RODRÍGUEZ, J. C.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1132766
Resumo: Background: SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient?s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group. Results: Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. Conclusion: Our study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.
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spelling Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.COVID 19SARS CoV 2NGS next generation sequencingCoronavirusMicrobiomePrevotellaBackground: SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient?s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group. Results: Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. Conclusion: Our study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.MARIA PAZ VENTERO, ISABIAL; RAFAEL R. C. CUADRAT, German Institute of Human Nutrition Potsdam-Rehbrücke; INMACULADA VIDAL, ISABIAL; BRUNO G. N. ANDRADE, Munster Technological University; CARMEN MOLINA-PARDINES, ISABIAL; JOSE M. HARO-MORENO, Universidad Miguel Hernández; FELIPE H. COUTINHO, Universidad Miguel Hernández; ESPERANZA MERINO, ISABIAL; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; CYNTHIA B. SILVEIRA, University of Miami; HAITHEM AFLI, Munster Technological University; MARIO LÓPEZ-PÉREZ, ISABIAL; JUAN CARLOS RODRÍGUEZ, ISABIAL.PAZ VENTERO, M.CUADRAT, R. R. C.VIDAL, I.ANDRADE, B. G. N.MOLINA-PARDINES, C.HARI-MORENO, J. M.COUTINHO, F. H.MERINO, E.REGITANO, L. C. de A.SILVEIRA, C. B.AFLI, H.LÓPEZ-PÉREZ, M.RODRÍGUEZ, J. C.2021-07-04T02:17:32Z2021-07-04T02:17:32Z2021-07-022021info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article10 p.Frontiers in Microbiology, v.12, 637430, mar. 2021http://www.alice.cnptia.embrapa.br/alice/handle/doc/113276610.3389/fmicb.2021.637430enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2021-07-04T02:17:43Zoai:www.alice.cnptia.embrapa.br:doc/1132766Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542021-07-04T02:17:43falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542021-07-04T02:17:43Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
title Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
spellingShingle Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
PAZ VENTERO, M.
COVID 19
SARS CoV 2
NGS next generation sequencing
Coronavirus
Microbiome
Prevotella
title_short Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
title_full Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
title_fullStr Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
title_full_unstemmed Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
title_sort Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
author PAZ VENTERO, M.
author_facet PAZ VENTERO, M.
CUADRAT, R. R. C.
VIDAL, I.
ANDRADE, B. G. N.
MOLINA-PARDINES, C.
HARI-MORENO, J. M.
COUTINHO, F. H.
MERINO, E.
REGITANO, L. C. de A.
SILVEIRA, C. B.
AFLI, H.
LÓPEZ-PÉREZ, M.
RODRÍGUEZ, J. C.
author_role author
author2 CUADRAT, R. R. C.
VIDAL, I.
ANDRADE, B. G. N.
MOLINA-PARDINES, C.
HARI-MORENO, J. M.
COUTINHO, F. H.
MERINO, E.
REGITANO, L. C. de A.
SILVEIRA, C. B.
AFLI, H.
LÓPEZ-PÉREZ, M.
RODRÍGUEZ, J. C.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv MARIA PAZ VENTERO, ISABIAL; RAFAEL R. C. CUADRAT, German Institute of Human Nutrition Potsdam-Rehbrücke; INMACULADA VIDAL, ISABIAL; BRUNO G. N. ANDRADE, Munster Technological University; CARMEN MOLINA-PARDINES, ISABIAL; JOSE M. HARO-MORENO, Universidad Miguel Hernández; FELIPE H. COUTINHO, Universidad Miguel Hernández; ESPERANZA MERINO, ISABIAL; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; CYNTHIA B. SILVEIRA, University of Miami; HAITHEM AFLI, Munster Technological University; MARIO LÓPEZ-PÉREZ, ISABIAL; JUAN CARLOS RODRÍGUEZ, ISABIAL.
dc.contributor.author.fl_str_mv PAZ VENTERO, M.
CUADRAT, R. R. C.
VIDAL, I.
ANDRADE, B. G. N.
MOLINA-PARDINES, C.
HARI-MORENO, J. M.
COUTINHO, F. H.
MERINO, E.
REGITANO, L. C. de A.
SILVEIRA, C. B.
AFLI, H.
LÓPEZ-PÉREZ, M.
RODRÍGUEZ, J. C.
dc.subject.por.fl_str_mv COVID 19
SARS CoV 2
NGS next generation sequencing
Coronavirus
Microbiome
Prevotella
topic COVID 19
SARS CoV 2
NGS next generation sequencing
Coronavirus
Microbiome
Prevotella
description Background: SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient?s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group. Results: Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. Conclusion: Our study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.
publishDate 2021
dc.date.none.fl_str_mv 2021-07-04T02:17:32Z
2021-07-04T02:17:32Z
2021-07-02
2021
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv Frontiers in Microbiology, v.12, 637430, mar. 2021
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1132766
10.3389/fmicb.2021.637430
identifier_str_mv Frontiers in Microbiology, v.12, 637430, mar. 2021
10.3389/fmicb.2021.637430
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1132766
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.format.none.fl_str_mv 10 p.
dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
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instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv cg-riaa@embrapa.br
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