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Altered infective competence of the human gut microbiome in COVID-19

BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome altera...

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Autores principales: de Nies, Laura, Galata, Valentina, Martin-Gallausiaux, Camille, Despotovic, Milena, Busi, Susheel Bhanu, Snoeck, Chantal J., Delacour, Lea, Budagavi, Deepthi Poornima, Laczny, Cédric Christian, Habier, Janine, Lupu, Paula-Cristina, Halder, Rashi, Fritz, Joëlle V., Marques, Taina, Sandt, Estelle, O’Sullivan, Marc Paul, Ghosh, Soumyabrata, Satagopam, Venkata, Krüger, Rejko, Fagherazzi, Guy, Ollert, Markus, Hefeng, Feng Q., May, Patrick, Wilmes, Paul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9995755/
https://www.ncbi.nlm.nih.gov/pubmed/36894986
http://dx.doi.org/10.1186/s40168-023-01472-7
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author de Nies, Laura
Galata, Valentina
Martin-Gallausiaux, Camille
Despotovic, Milena
Busi, Susheel Bhanu
Snoeck, Chantal J.
Delacour, Lea
Budagavi, Deepthi Poornima
Laczny, Cédric Christian
Habier, Janine
Lupu, Paula-Cristina
Halder, Rashi
Fritz, Joëlle V.
Marques, Taina
Sandt, Estelle
O’Sullivan, Marc Paul
Ghosh, Soumyabrata
Satagopam, Venkata
Krüger, Rejko
Fagherazzi, Guy
Ollert, Markus
Hefeng, Feng Q.
May, Patrick
Wilmes, Paul
author_facet de Nies, Laura
Galata, Valentina
Martin-Gallausiaux, Camille
Despotovic, Milena
Busi, Susheel Bhanu
Snoeck, Chantal J.
Delacour, Lea
Budagavi, Deepthi Poornima
Laczny, Cédric Christian
Habier, Janine
Lupu, Paula-Cristina
Halder, Rashi
Fritz, Joëlle V.
Marques, Taina
Sandt, Estelle
O’Sullivan, Marc Paul
Ghosh, Soumyabrata
Satagopam, Venkata
Krüger, Rejko
Fagherazzi, Guy
Ollert, Markus
Hefeng, Feng Q.
May, Patrick
Wilmes, Paul
author_sort de Nies, Laura
collection PubMed
description BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-023-01472-7.
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spelling pubmed-99957552023-03-09 Altered infective competence of the human gut microbiome in COVID-19 de Nies, Laura Galata, Valentina Martin-Gallausiaux, Camille Despotovic, Milena Busi, Susheel Bhanu Snoeck, Chantal J. Delacour, Lea Budagavi, Deepthi Poornima Laczny, Cédric Christian Habier, Janine Lupu, Paula-Cristina Halder, Rashi Fritz, Joëlle V. Marques, Taina Sandt, Estelle O’Sullivan, Marc Paul Ghosh, Soumyabrata Satagopam, Venkata Krüger, Rejko Fagherazzi, Guy Ollert, Markus Hefeng, Feng Q. May, Patrick Wilmes, Paul Microbiome Research BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-023-01472-7. BioMed Central 2023-03-09 /pmc/articles/PMC9995755/ /pubmed/36894986 http://dx.doi.org/10.1186/s40168-023-01472-7 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
de Nies, Laura
Galata, Valentina
Martin-Gallausiaux, Camille
Despotovic, Milena
Busi, Susheel Bhanu
Snoeck, Chantal J.
Delacour, Lea
Budagavi, Deepthi Poornima
Laczny, Cédric Christian
Habier, Janine
Lupu, Paula-Cristina
Halder, Rashi
Fritz, Joëlle V.
Marques, Taina
Sandt, Estelle
O’Sullivan, Marc Paul
Ghosh, Soumyabrata
Satagopam, Venkata
Krüger, Rejko
Fagherazzi, Guy
Ollert, Markus
Hefeng, Feng Q.
May, Patrick
Wilmes, Paul
Altered infective competence of the human gut microbiome in COVID-19
title Altered infective competence of the human gut microbiome in COVID-19
title_full Altered infective competence of the human gut microbiome in COVID-19
title_fullStr Altered infective competence of the human gut microbiome in COVID-19
title_full_unstemmed Altered infective competence of the human gut microbiome in COVID-19
title_short Altered infective competence of the human gut microbiome in COVID-19
title_sort altered infective competence of the human gut microbiome in covid-19
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9995755/
https://www.ncbi.nlm.nih.gov/pubmed/36894986
http://dx.doi.org/10.1186/s40168-023-01472-7
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