Salivary fungal community types (mycotypes) with distinct ecological and oral disease associations

A broad range of fungi have been detected in molecular surveys of the oral mycobiome. However, it is not clear which of these fungi represent clinically significant commensals. In this cross-sectional analysis we use intragenic transcribed spacer 1 amplicon sequencing to evaluate the composition of the salivary mycobiome in 59 subjects, 36 of which were scheduled to receive cancer chemotherapy. An analysis of the broad population structure of fungal communities in the whole cohort identified two well demarcated genus-level community types (mycotypes), with Candida and Malassezia as the main taxa driving cluster partitioning. The Candida mycotype was more frequently seen in subjects with cancer and was positively associated with steroid use, smoking, wearing a removable prosthesis and Plaque Index, which was the only variable that retained an independent significant association with the Candida mycotype. Mycotypes were also associated with metabolically distinct bacteria indicative of different oral environments, with aciduric/acidogenic species enriched in Candida mycotype subjects, while inflammophilic bacteria were increased in subjects harboring the Malassezia mycotype. Consistent with these findings, Candida mycotype fungal and coexisting bacterial communities had lower diversity and Candida positively correlated with presence and severity of caries, while Malassezia correlated with presence of deep periodontal pockets. Community types were confirmed in an independent cohort of 24 subjects, in which cultivation revealed Malassezia as viable oral mycobiome members, although the low abundance Malassezia sympodialis was the only species recovered. There was high degree of concordance between the molecular detection and cultivability of Candida, while cultivation showed low sensitivity for detection of the Malassezia mycotype. Overall, our work provides insights into the oral mycobiome landscape revealing two community classes with apparently distinct ecological constraints and specific associations with clinical parameters. The salivary mycotype classification could represent a useful diagnostic tool when included in multivariate predictive models for oral diseases.