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

Jiarui Li; Qiuyu Jing; Jie Li; Mingxi Hua; Lin Di; Chuan Song; Yanyi Huang; Jianbin Wang; Chen Chen; Angela Ruohao Wu

doi:10.1186/s40168-022-01447-0

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

Microbiome. 2023 Mar 3;11(1):38. doi: 10.1186/s40168-022-01447-0.

Authors

Jiarui Li^#¹, Qiuyu Jing^#², Jie Li^#³, Mingxi Hua^#¹, Lin Di^{4

5}, Chuan Song¹, Yanyi Huang^{5

6

7}, Jianbin Wang³, Chen Chen⁸, Angela Ruohao Wu^{9

10

11}

Affiliations

¹ Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100015, China.
² Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China.
³ School of Life Sciences, Tsinghua University, Beijing, 100084, China.
⁴ School of Life Sciences, Peking University, Beijing, 100871, China.
⁵ Biomedical Pioneering Innovation Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
⁶ College of Chemistry and Molecular Engineering, Beijing, 100871, China.
⁷ Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, 518132, China.
⁸ Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, 100038, Beijing, China. chenchen1@ccmu.edu.cn.
⁹ Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China. angelawu@ust.hk.
¹⁰ Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China. angelawu@ust.hk.
¹¹ Hong Kong Branch of Guangdong Southern Marine Science and Engineering Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China. angelawu@ust.hk.

^# Contributed equally.

Abstract

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. Video Abstract.

Keywords: COVID-19; Gut; Human microbiota; SARS-CoV-2; Upper respiratory tract.

Publication types

Video-Audio Media
Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Gastrointestinal Microbiome*
Humans
Microbiota*
Nose
SARS-CoV-2