Nasopharyngeal microbial communities of patients infected with SARS-CoV-2 that developed COVID-19.
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , , , , , |
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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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 |
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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) instacron:EMBRAPA |
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Empresa Brasileira de Pesquisa Agropecuária (Embrapa) |
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EMBRAPA |
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EMBRAPA |
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Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) |
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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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1794503506636308480 |