Journal Article

Prediction of baseline oral microbiota for clinical classification post Omicron variant of SARS-CoV-2 infection

Sun, Ying, Wang, Xueping, Wang, Daming, Ren, Zhigang, Yu, Zujiang, Liu, Bowen, Wang, Haiyu, Zou, Yawen, Luo, Hong, Liu, Shanshuo, Wu, Zhongwen, Zhou, Yongjian, Gao, Feng, Sun, Junyi, Li, Lei, Yu, Jia

2026

Overview

Oral microbiota is related to the severity and recovery of SARS-CoV-2 infection. This study aims to predict clinical classification after SARS-CoV-2 infection using oral microbiota before infection. Herein, we collected tongue-coating samples before infection and then monitored clinical information after infection. Oral microbiota was detected by MiSeq sequencing. We randomly assigned participants from Zhengzhou into discovery and validation cohorts to develop a predictive model and conducted cross-region verification using Xinyang and Hangzhou cohorts. Sixteen asymptomatic patients (AP), 257 mild patients (MP), 106 common patients (CP), and 7 severe patients (SP) were enrolled. Oral microbiota diversity was decreased in CP versus MP. At genus level, 11 microorganisms, including Rothia and Gemella , were increased, while 5 microorganisms, including Selenomonas and Lachnoanaerobaculum , were decreased in CP versus MP. Moreover, the classifier based on 15 optimal markers showed high prediction efficiency in discovery cohort (area under the curve [AUC]: 98.35%), validation cohort (AUC: 81.91%), Xinyang cohort (AUC: 74.34%), and Hangzhou cohort (AUC: 94.44%). Interestingly, a higher abundance of Selenomonas was associated with milder clinical symptoms. In conclusion, our study established a good model to predict clinical classification after SARS-CoV-2 infection using oral microbiota before infection, providing a novel strategy for precise prevention and treatment.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/326 / 692/308/53 / Adult / Aged / Asymptomatic / Bacteria / Blood / China / Chronic obstructive pulmonary disease / Classification / Clinical classification / COVID-19 / COVID-19 - classification / COVID-19 - diagnosis / COVID-19 - microbiology / COVID-19 - virology / Female / Humanities and Social Sciences / Humans / Immune system / Infections / Male / Microbial marker / Microbiota / Microorganisms / Middle Aged / Mouth - microbiology / multidisciplinary / Neutrophils / Omicron variant / Oral microbiota / Patients / Prediction models / Predictive efficiency / SARS-CoV-2 - isolation & purification / Science / Science (multidisciplinary) / Selenomonas / Severe acute respiratory syndrome coronavirus 2 / Severity of Illness Index