Integrated gut virome and bacteriome dynamics in COVID-19 patients

Gut Microbes

Ning Zhang¹  Yuhuan Gong¹  Jin Yan²  Fanping Meng²  Linxiang Yu²  Shaogeng Zhang²  Penghui Yang²  Changqing Bai²  Zhu Chen²  Guanglin Lei²  Cheng Wang³  Jingjing Lu⁴  Jiabao Cao⁴  Jun Wang⁴  Lianpan Dai⁴  Na Zhao⁴  Yuhai Bi⁴  Yi Shi⁴  Yuqing Zhang⁴  Kun Xu⁵ 

[1] Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences;Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases;First Medical Center of Chinese PLA General Hospital;Institute of Microbiology, Chinese Academy of Sciences;School of Tropical Medicine and Laboratory Medicine, the First Affiliated Hospital, Hainan Medical University;

关键词: covid-19;    genetic mutation;    virome;    bacteriome;    dysbiosis;   

DOI  :  10.1080/19490976.2021.1887722

来源: DOAJ

【 摘 要 】

SARS-CoV-2 is the cause of the current global pandemic of COVID-19; this virus infects multiple organs, such as the lungs and gastrointestinal tract. The microbiome in these organs, including the bacteriome and virome, responds to infection and might also influence disease progression and treatment outcome. In a cohort of 13 COVID-19 patients in Beijing, China, we observed that the gut virome and bacteriome in the COVID-19 patients were notably different from those of five healthy controls. We identified a bacterial dysbiosis signature by observing reduced diversity and viral shifts in patients, and among the patients, the bacterial/viral compositions were different between patients of different severities, although these differences are not entirely distinguishable from the effect of antibiotics. Severe cases of COVID-19 exhibited a greater abundance of opportunistic pathogens but were depleted for butyrate-producing groups of bacteria compared with mild to moderate cases. We replicated our findings in a mouse COVID-19 model, confirmed virome differences and bacteriome dysbiosis due to SARS-CoV-2 infection, and observed that immune/infection-related genes were differentially expressed in gut epithelial cells during infection, possibly explaining the virome and bacteriome dynamics. Our results suggest that the components of the microbiome, including the bacteriome and virome, are affected by SARS-CoV-2 infections, while their compositional signatures could reflect or even contribute to disease severity and recovery processes.

【 授权许可】

Unknown