Assessment of Microbiota in the Gut and Upper Respiratory Tract Associated with SARS-CoV-2 Infection

The human microbiome plays an important role in modulating the host metabolism and immune system. A systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota can broaden our understanding of the infection and host response. We find altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are in direct correlation with viral load and associated with disease severity. Compared to the URT, gut microbiota is more sensitive to SARS-CoV-2 infection. Moreover, we observed a higher risk of potential bacterial coinfections, as well as higher risk of antibiotics resistance in correlation with these microbial alterations. These observations indicate that microbiota can be a potential indicator of the disease status, and it is necessary to evaluate potential coinfections and antibiotic resistance in the management of COVID-19 patients.Funding: This work was supported by National Natural Science Foundation of China (21675098, 21927802, 21525521), Ministry of Science and Technology of China (2018YFA0800200, 2018YFA0108100, 2018YFC1002300), 2018 Beijing Brain Initiation (Z181100001518004), Beijing Advanced Innovation Center for Structural Biology, Beijing Advanced Innovation Center for Genomics, HKUST’s start-up and initiation grants (Hong Kong University Grants Committee), Hong Kong Research Grants Council Theme-based Research Scheme (RGC TBRS T12-704/16R-2) and Collaborative Research Fund (RGC CRF C6002-17G), Hong Kong RGC Early Career Support Scheme (RGC ECS 26101016), Hong Kong Epigenomics Project (LKCCFL18SC01-E), and HKUST BDBI Labs. Conflict of Interest: The authors declare no conflicts of interest.Ethical Approval: This study was approved by the Ethics Committee of Beijing Ditan Hospital, Capital Medical University (No. KT2020-006-01).