Perturbations in gut and respiratory microbiota in COVID-19 and influenza patients: a systematic review and meta-analysis

Xiu-Jie Chu; Dan-Dan Song; Ming-Hua Zhou; Xiu-Zhi Chen; Na Chu; Ming Li; Bao-Zhu Li; Song-Hui Liu; Sai Hou; Jia-Bing Wu; Lei Gong

doi:10.3389/fmed.2024.1301312

Perturbations in gut and respiratory microbiota in COVID-19 and influenza patients: a systematic review and meta-analysis

Front Med (Lausanne). 2024 Feb 9:11:1301312. doi: 10.3389/fmed.2024.1301312. eCollection 2024.

Authors

Xiu-Jie Chu^#¹, Dan-Dan Song^#¹, Ming-Hua Zhou^#², Xiu-Zhi Chen¹, Na Chu¹, Ming Li¹, Bao-Zhu Li², Song-Hui Liu³, Sai Hou¹, Jia-Bing Wu¹, Lei Gong¹

Affiliations

¹ Department of Acute Infectious Disease Prevention and Control, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.
² Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.
³ School of Public Health, Bengbu Medical College, Bengbu, Anhui, China.

^# Contributed equally.

Abstract

Objectives: Coronavirus disease-19 (COVID-19)/influenza poses unprecedented challenges to the global economy and healthcare services. Numerous studies have described alterations in the microbiome of COVID-19/influenza patients, but further investigation is needed to understand the relationship between the microbiome and these diseases. Herein, through systematic comparison between COVID-19 patients, long COVID-19 patients, influenza patients, no COVID-19/influenza controls and no COVID-19/influenza patients, we conducted a comprehensive review to describe the microbial change of respiratory tract/digestive tract in COVID-19/influenza patients.

Methods: We systematically reviewed relevant literature by searching the PubMed, Embase, and Cochrane Library databases from inception to August 12, 2023. We conducted a comprehensive review to explore microbial alterations in patients with COVID-19/influenza. In addition, the data on α-diversity were summarized and analyzed by meta-analysis.

Results: A total of 134 studies comparing COVID-19 patients with controls and 18 studies comparing influenza patients with controls were included. The Shannon indices of the gut and respiratory tract microbiome were slightly decreased in COVID-19/influenza patients compared to no COVID-19/influenza controls. Meanwhile, COVID-19 patients with more severe symptoms also exhibited a lower Shannon index versus COVID-19 patients with milder symptoms. The intestinal microbiome of COVID-19 patients was characterized by elevated opportunistic pathogens along with reduced short-chain fatty acid (SCFAs)-producing microbiota. Moreover, Enterobacteriaceae (including Escherichia and Enterococcus) and Lactococcus, were enriched in the gut and respiratory tract of COVID-19 patients. Conversely, Haemophilus and Neisseria showed reduced abundance in the respiratory tract of both COVID-19 and influenza patients.

Conclusion: In this systematic review, we identified the microbiome in COVID-19/influenza patients in comparison with controls. The microbial changes in influenza and COVID-19 are partly similar.

Keywords: COVID-19; gut; influenza; microbiome; respiratory tract.

Publication types

Systematic Review

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by the Emergency research project of novel coronavirus infection of Anhui province (2022e07020071) and Research funds of Center for Big Data and Population Health of IHM (JKS2022023).