Diagnostic efficiency of oral microbiome and serum metabolome in patients with SARS-CoV-2 omicron variant infection and recovery

SARS-CoV-2 variants pose a threat to human health. However, alterations in the oral microbiome and serum metabolome of patients with the SARS-CoV-2 omicron variant (OV) have not been reported. In total, 349 patients with OV, 72 patients with original strain (OS), and 400 healthy controls (HC) were enrolled. Subsequently, 262 patients with OV and 62 with OS completed the follow-up. The oral microbiota was detected using MiSeq sequencing, and serum metabolomics was detected and analyzed. Oral microbial diversity increased in the OV. Compared with HC, 20 genera, including Prevonella and Atopobium increased, whereas 23 genera, including Neisseria and Haemophilus decreased. The classifier based on six optimal microbial markers had a high diagnostic efficiency in the discovery cohort (area under the curve (AUC) of 97.73%) and validation cohort (AUC of 93.06%) between OV and HC. Importantly, compared with OS, OV induced an increase in Fusobacterium. Compared with HC, five metabolites, including L-arginine, were elevated, while prenylcysteine was decreased in OV. The classifier based on the six metabolites had high diagnostic efficiency in the discovery cohort (AUC of 99.3%) and validation cohort (AUC of 99.77%) between OV and HC. In conclusion, this study is the first to characterize oral microbiota and serum metabolites in OV and to construct non-invasive diagnostic models to provide new strategies for the prevention and control of coronavirus variants.