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Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection

BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding o...

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Autores principales: Li, Jiarui, Jing, Qiuyu, Li, Jie, Hua, Mingxi, Di, Lin, Song, Chuan, Huang, Yanyi, Wang, Jianbin, Chen, Chen, Wu, Angela Ruohao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9982190/
https://www.ncbi.nlm.nih.gov/pubmed/36869345
http://dx.doi.org/10.1186/s40168-022-01447-0
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author Li, Jiarui
Jing, Qiuyu
Li, Jie
Hua, Mingxi
Di, Lin
Song, Chuan
Huang, Yanyi
Wang, Jianbin
Chen, Chen
Wu, Angela Ruohao
author_facet Li, Jiarui
Jing, Qiuyu
Li, Jie
Hua, Mingxi
Di, Lin
Song, Chuan
Huang, Yanyi
Wang, Jianbin
Chen, Chen
Wu, Angela Ruohao
author_sort Li, Jiarui
collection PubMed
description BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity. RESULTS: We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputa, and 152 fecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in the upper respiratory tract renders a high risk of antibiotic resistance. Longitudinally, the microbial composition remains relatively stable during the study period. CONCLUSIONS: Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for the prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, a longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01447-0.
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spelling pubmed-99821902023-03-03 Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection Li, Jiarui Jing, Qiuyu Li, Jie Hua, Mingxi Di, Lin Song, Chuan Huang, Yanyi Wang, Jianbin Chen, Chen Wu, Angela Ruohao Microbiome Research BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity. RESULTS: We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputa, and 152 fecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in the upper respiratory tract renders a high risk of antibiotic resistance. Longitudinally, the microbial composition remains relatively stable during the study period. CONCLUSIONS: Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for the prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, a longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01447-0. BioMed Central 2023-03-03 /pmc/articles/PMC9982190/ /pubmed/36869345 http://dx.doi.org/10.1186/s40168-022-01447-0 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
Li, Jiarui
Jing, Qiuyu
Li, Jie
Hua, Mingxi
Di, Lin
Song, Chuan
Huang, Yanyi
Wang, Jianbin
Chen, Chen
Wu, Angela Ruohao
Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
title Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
title_full Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
title_fullStr Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
title_full_unstemmed Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
title_short Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection
title_sort assessment of microbiota in the gut and upper respiratory tract associated with sars-cov-2 infection
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9982190/
https://www.ncbi.nlm.nih.gov/pubmed/36869345
http://dx.doi.org/10.1186/s40168-022-01447-0
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