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Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host

Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome stu...

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Autores principales: Lloréns-Rico, Verónica, Gregory, Ann C., Van Weyenbergh, Johan, Jansen, Sander, Van Buyten, Tina, Qian, Junbin, Braz, Marcos, Menezes, Soraya Maria, Van Mol, Pierre, Vanderbeke, Lore, Dooms, Christophe, Gunst, Jan, Hermans, Greet, Meersseman, Philippe, Wauters, Els, Neyts, Johan, Lambrechts, Diether, Wauters, Joost, Raes, Jeroen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8556379/
https://www.ncbi.nlm.nih.gov/pubmed/34716338
http://dx.doi.org/10.1038/s41467-021-26500-8
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author Lloréns-Rico, Verónica
Gregory, Ann C.
Van Weyenbergh, Johan
Jansen, Sander
Van Buyten, Tina
Qian, Junbin
Braz, Marcos
Menezes, Soraya Maria
Van Mol, Pierre
Vanderbeke, Lore
Dooms, Christophe
Gunst, Jan
Hermans, Greet
Meersseman, Philippe
Wauters, Els
Neyts, Johan
Lambrechts, Diether
Wauters, Joost
Raes, Jeroen
author_facet Lloréns-Rico, Verónica
Gregory, Ann C.
Van Weyenbergh, Johan
Jansen, Sander
Van Buyten, Tina
Qian, Junbin
Braz, Marcos
Menezes, Soraya Maria
Van Mol, Pierre
Vanderbeke, Lore
Dooms, Christophe
Gunst, Jan
Hermans, Greet
Meersseman, Philippe
Wauters, Els
Neyts, Johan
Lambrechts, Diether
Wauters, Joost
Raes, Jeroen
author_sort Lloréns-Rico, Verónica
collection PubMed
description Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n = 58) and lower (n = 35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We find that time in the intensive care unit and type of oxygen support, as well as associated treatments such as antibiotic usage, explain the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load has a reduced impact. Specifically, mechanical ventilation is linked to altered community structure and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomics of the lower respiratory tract of COVID-19 patients identifies specific oral bacteria in physical association with proinflammatory immune cells, which show higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
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spelling pubmed-85563792021-11-15 Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host Lloréns-Rico, Verónica Gregory, Ann C. Van Weyenbergh, Johan Jansen, Sander Van Buyten, Tina Qian, Junbin Braz, Marcos Menezes, Soraya Maria Van Mol, Pierre Vanderbeke, Lore Dooms, Christophe Gunst, Jan Hermans, Greet Meersseman, Philippe Wauters, Els Neyts, Johan Lambrechts, Diether Wauters, Joost Raes, Jeroen Nat Commun Article Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n = 58) and lower (n = 35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We find that time in the intensive care unit and type of oxygen support, as well as associated treatments such as antibiotic usage, explain the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load has a reduced impact. Specifically, mechanical ventilation is linked to altered community structure and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomics of the lower respiratory tract of COVID-19 patients identifies specific oral bacteria in physical association with proinflammatory immune cells, which show higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients. Nature Publishing Group UK 2021-10-29 /pmc/articles/PMC8556379/ /pubmed/34716338 http://dx.doi.org/10.1038/s41467-021-26500-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Lloréns-Rico, Verónica
Gregory, Ann C.
Van Weyenbergh, Johan
Jansen, Sander
Van Buyten, Tina
Qian, Junbin
Braz, Marcos
Menezes, Soraya Maria
Van Mol, Pierre
Vanderbeke, Lore
Dooms, Christophe
Gunst, Jan
Hermans, Greet
Meersseman, Philippe
Wauters, Els
Neyts, Johan
Lambrechts, Diether
Wauters, Joost
Raes, Jeroen
Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
title Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
title_full Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
title_fullStr Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
title_full_unstemmed Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
title_short Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
title_sort clinical practices underlie covid-19 patient respiratory microbiome composition and its interactions with the host
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8556379/
https://www.ncbi.nlm.nih.gov/pubmed/34716338
http://dx.doi.org/10.1038/s41467-021-26500-8
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