Open AccessCharacterization of the Human Oropharyngeal Microbiomes in SARS‐CoV‐2 Infection and Recovery Patients
Author(s) -
Gao Ming,
Wang Haiyu,
Luo Hong,
Sun Ying,
Wang Ling,
Ding Suying,
Ren Hongyan,
Gang Jiaqi,
Rao Benchen,
Liu Shanshuo,
Wang Xuemei,
Gao Xinxin,
Li Mengyi,
Zou Yawen,
Liu Chao,
Yuan Chengyu,
Sun Jiarui,
Cui Guangying,
Ren Zhigang
Publication year - 2021
Publication title -
advanced science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.388
H-Index - 100
ISSN - 2198-3844
DOI - 10.1002/advs.202102785
Subject(s) - microbiome , covid-19 , biology , human microbiome , medicine , immunology , disease , bioinformatics , infectious disease (medical specialty)
Respiratory tract microbiome is closely related to respiratory tract infections, while characterization of oropharyngeal microbiome in recovered coronavirus disease 2019 (COVID‐19) patients is not studied. Herein, oropharyngeal swabs are collected from confirmed cases (CCs) with COVID‐19 (73 subjects), suspected cases (SCs) (36), confirmed cases who recovered (21), suspected cases who recovered (36), and healthy controls (Hs) (140) and then completed MiSeq sequencing. Oropharyngeal microbial α ‐diversity is markedly reduced in CCs versus Hs. Opportunistic pathogens are increased, while butyrate‐producing genera are decreased in CCs versus Hs. The classifier based on eight optimal microbial markers is constructed through a random forest model and reached great diagnostic efficacy in both discovery and validation cohorts. Notably, the classifier successfully diagnosed SCs with positive IgG antibody as CCs and is demonstrated from the perspective of the microbiome. Importantly, several genera with significant differences gradually increase and decrease along with recovery from COVID‐19. Forty‐four oropharyngeal operational taxonomy units (OTUs) are closely correlated with 11 clinical indicators of SARS‐CoV‐2 infection and Hs based on Spearman correlation analysis. Together, this research is the first to characterize oropharyngeal microbiota in recovered COVID‐19 cases and suspected cases, to successfully construct and validate the diagnostic model for COVID‐19 and to depict the correlations between microbial OTUs and clinical indicators.