AUTHOR=Shi Yong-Lin , He Mao-Zhang , Han Mao-Zhen , Gui Hong-Ya , Wang Peng , Yu Jun-Ling , Ge Ying-Lu , Sun Yong , Huang Sheng-Hai 

TITLE=Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=Volume 12 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2022.824578

DOI=10.3389/fcimb.2022.824578

ISSN=2235-2988

ABSTRACT=Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in the mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobiu and Pseudomonas stutzeri, and depletion of Sphingononas yabuuchiae, Agrobacterium sullae and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which Pseudomonas veronii, Pseudomonas fragi and Sphingomonas yabuuchiae were identified as the most prominent signature for their depletion in COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus which were highly enriched in the COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several clinical routine blood indicators, indicating that the oral cavity might acts as a natural reservoir for pathogens to aggravate virus infection in the respiratory tract of COVID-19 patients. We also found the diver taxa of Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, we found that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity.