Dynamic alterations of oral fungal microbiota in Omicron infected patients

Oral fungal microbiota plays an important role in many diseases, however, the role of oral fungal microorganisms in the development of patients infected with Omicron has not been reported. A total of 963 tongue coating samples were prospectively included in this study, and finally 336 samples from patients infected Omicron variant (PIOV), 234 samples from recovered patients infected with Omicron (RP), 71 samples from patients infected original strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (PIOS), 299 samples from healthy controls (HC) completed internal transcribed spacer (ITS) sequencing after screening and quality control. By comparing the difference of oral fungal microorganisms between PIOV, RP and HC, we found that with the recovery of PIOV, their oral fungal microecological diversity increased gradually. Besides, at the species level, there were 24 oral fungal species such as Zanclospora_jonesii increased gradually, while there were 24 oral fungal species such as Saccharomyces_cerevisiae decreased gradually. In addition, by comparing PIOS and PIOV, we found that the alpha diversity of oral fungal microorganisms in PIOV was significantly lower than PIOS and the main species of the two groups were different. At the same time, we randomly divided PIOV and HC into training and validation set. Based on random forest model and five-fold cross-validation, we identified three optimal microbial markers of oral fungi and constructed a diagnostic model of PIOV. The area under the curve (AUC) value of PIOV group was 99.01% in discovery phase and 97.84% in verification phase. In summary, based on large-scale samples, this study is the first to elucidate the characteristics of oral fungal microbiota changes during PIOV recovery and establish a supplemental non-invasive diagnostic model for PIOV based on the oral fungal microbiome.