Altered oral and gut microbiota and its association with SARS-CoV-2 viral load in COVID-19 patients during hospitalization

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Abstract

The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.

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Author and article information

Contributors

Jiahai Lu:

ORCID: http://orcid.org/0000-0002-8593-3402

lujiahai@mail.sysu.edu.cn

Cheng Guo:

ORCID: http://orcid.org/0000-0002-6602-8810

cg2984@cumc.columbia.edu

Hong Shan:

ORCID: http://orcid.org/0000-0001-6640-1390

shanhong@mail.sysu.edu.cn

Xi Huang:

ORCID: http://orcid.org/0000-0002-4829-8390

huangxi6@mail.sysu.edu.cn

Journal

Journal ID (nlm-ta): NPJ Biofilms Microbiomes

Journal ID (iso-abbrev): NPJ Biofilms Microbiomes

Title: NPJ Biofilms and Microbiomes

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2055-5008

Publication date (Electronic): 22 July 2021

Publication date PMC-release: 22 July 2021

Publication date Collection: 2021

Volume: 7

Electronic Location Identifier: 61

Affiliations

[1 ]GRID grid.452859.7, Center for Infection and Immunity, , The Fifth Affiliated Hospital, Sun Yat-sen University, ; Zhuhai, Guangdong China

[2 ]GRID grid.12981.33, ISNI 0000 0001 2360 039X, School of public health, , Sun Yat-sen University, ; Guangzhou, Guangdong China

[3 ]GRID grid.452859.7, Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Imaging, and Department of Interventional Medicine, , The Fifth Affiliated Hospital, Sun Yat-sen University, ; Zhuhai, Guangdong China

[4 ]GRID grid.511004.1, Southern Marine Science and Engineering Guangdong Laboratory, ; Zhuhai, Guangdong China

[5 ]GRID grid.410741.7, National Clinical Research Center for Infectious Disease, , Shenzhen Third People’ s Hospital; The Second Affiliated Hospital of Southern University of Science and Technology, ; Shenzhen, Guangdong China

[6 ]GRID grid.21729.3f, ISNI 0000000419368729, Center for Infection and Immunity, Mailman School of Public Health, , Columbia University, ; New York, NY USA

Author information

Xiaomin Cheng http://orcid.org/0000-0001-9111-6954

Jiahai Lu http://orcid.org/0000-0002-8593-3402

Cheng Guo http://orcid.org/0000-0002-6602-8810

Hong Shan http://orcid.org/0000-0001-6640-1390

Xi Huang http://orcid.org/0000-0002-4829-8390

Article

Publisher ID: 232

DOI: 10.1038/s41522-021-00232-5

PMC ID: 8298611

PubMed ID: 34294722

SO-VID: 648f0be1-dd13-4c22-aefc-c2e97624961f

License:

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/.

History

Date received : 23 January 2021

Date accepted : 1 July 2021

Funding

Funded by: National Natural Science Foundation of China (82072062), National Science and Technology Key Projects for Major Infectious Diseases (2017ZX10302301-002), Guangzhou Science and Technology Planning Project (201704020226 and 201604020006), National Key Research and Development Program of China (2016YFC1200105), The Three Major Scientific Research Projects of Sun Yat-sen University (20200326236), Guangdong Scientific and Technological Research Project for COVID-19 containment (2020A111128022, 2020B111112003), Guangdong Scientific and Technological Research for COVID-19 (202020012612200001), Zhuhai Scientific and Technological Research Project for COVID-19 containment (ZH22036302200029PWC).