Composition of saliva metabolome is significantly associated with SARS-CoV2 infection and with severity of COVID-19 disease

Background The metabolome of COVID-19 patients has been studied sparsely, with most research focusing on a limited number of plasma metabolites or small cohorts. This is the first study to test saliva metabolites in COVID-19 patients in a comprehensive way, revealing significant changes linked to disease severity and highlighting saliva is potential as a non-invasive diagnostic tool. Methods We included 30 asymptomatic subjects with no prior COVID-19 infection or vaccination, 102 patients with mild SARS-CoV-2 infection, and 61 hospitalized patients with confirmed SARS-CoV-2 status. Saliva samples were analyzed using hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS/MS) in positive and negative ionization modes. Results Significant changes in metabolites were identified in COVID-19 patients, with distinct patterns based on disease severity. Healthy individuals exhibited a well-regulated bacterial network, while severe cases showed disordered microbial networks. Elevated dipeptides such as Val-Glu and Met-Gln in moderate cases suggest specific protease activity related to SARS-CoV-2. Increased acetylated amino acids like N-Acetylserine and N-Acetylhistidine indicate potential biomarkers for stress and disease severity. Bacterial metabolites, including muramic acid and indole-3-carboxaldehyde, were higher in mild-moderate cases, indicating oral microbiota changes. In severe cases, polyamines and organ damage-related metabolites, such as N-acetylspermine and 3-methylcytidine, were significantly increased. Interestingly, metabolites reduced in moderate cases were elevated in severe cases. Conclusions Saliva metabolomics offers insight into disease progression and potential biomarkers for COVID-19.