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Metagenomic assessment of gut microbial communities and risk of severe COVID-19
The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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American Journal Experts
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9176657/ https://www.ncbi.nlm.nih.gov/pubmed/35677075 http://dx.doi.org/10.21203/rs.3.rs-1717624/v1 |
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author | Lai, Peggy Nguyen, Long Okin, Daniel Drew, David Battista, Vincent Jesudasen, Sirus Kuntz, Thomas Bhosle, Amrisha Thompson, Kelsey Reinicke, Trenton Lo, Chun-Han Woo, Jacqueline Caraballo, Alexander Berra, Lorenzo Vieira, Jacob Huang, Ching-Ying Adhikari, Upasana Das Kim, Minsik Sui, Hui-Yu Magicheva-Gupta, Marina McIver, Lauren Goldberg, Marcia Kwon, Douglas Huttenhower, Curtis Chan, Andrew |
author_facet | Lai, Peggy Nguyen, Long Okin, Daniel Drew, David Battista, Vincent Jesudasen, Sirus Kuntz, Thomas Bhosle, Amrisha Thompson, Kelsey Reinicke, Trenton Lo, Chun-Han Woo, Jacqueline Caraballo, Alexander Berra, Lorenzo Vieira, Jacob Huang, Ching-Ying Adhikari, Upasana Das Kim, Minsik Sui, Hui-Yu Magicheva-Gupta, Marina McIver, Lauren Goldberg, Marcia Kwon, Douglas Huttenhower, Curtis Chan, Andrew |
author_sort | Lai, Peggy |
collection | PubMed |
description | The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or “long COVID”, suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention. |
format | Online Article Text |
id | pubmed-9176657 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Journal Experts |
record_format | MEDLINE/PubMed |
spelling | pubmed-91766572022-06-09 Metagenomic assessment of gut microbial communities and risk of severe COVID-19 Lai, Peggy Nguyen, Long Okin, Daniel Drew, David Battista, Vincent Jesudasen, Sirus Kuntz, Thomas Bhosle, Amrisha Thompson, Kelsey Reinicke, Trenton Lo, Chun-Han Woo, Jacqueline Caraballo, Alexander Berra, Lorenzo Vieira, Jacob Huang, Ching-Ying Adhikari, Upasana Das Kim, Minsik Sui, Hui-Yu Magicheva-Gupta, Marina McIver, Lauren Goldberg, Marcia Kwon, Douglas Huttenhower, Curtis Chan, Andrew Res Sq Article The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or “long COVID”, suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention. American Journal Experts 2022-06-07 /pmc/articles/PMC9176657/ /pubmed/35677075 http://dx.doi.org/10.21203/rs.3.rs-1717624/v1 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. |
spellingShingle | Article Lai, Peggy Nguyen, Long Okin, Daniel Drew, David Battista, Vincent Jesudasen, Sirus Kuntz, Thomas Bhosle, Amrisha Thompson, Kelsey Reinicke, Trenton Lo, Chun-Han Woo, Jacqueline Caraballo, Alexander Berra, Lorenzo Vieira, Jacob Huang, Ching-Ying Adhikari, Upasana Das Kim, Minsik Sui, Hui-Yu Magicheva-Gupta, Marina McIver, Lauren Goldberg, Marcia Kwon, Douglas Huttenhower, Curtis Chan, Andrew Metagenomic assessment of gut microbial communities and risk of severe COVID-19 |
title | Metagenomic assessment of gut microbial communities and risk of severe COVID-19 |
title_full | Metagenomic assessment of gut microbial communities and risk of severe COVID-19 |
title_fullStr | Metagenomic assessment of gut microbial communities and risk of severe COVID-19 |
title_full_unstemmed | Metagenomic assessment of gut microbial communities and risk of severe COVID-19 |
title_short | Metagenomic assessment of gut microbial communities and risk of severe COVID-19 |
title_sort | metagenomic assessment of gut microbial communities and risk of severe covid-19 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9176657/ https://www.ncbi.nlm.nih.gov/pubmed/35677075 http://dx.doi.org/10.21203/rs.3.rs-1717624/v1 |
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