Filtration-enriched metabolites and their association with salivary microbiota: a combined two-cohort analysis

We aimed to identify significantly reduced metabolites (SRMs) in saliva by filtration and to analyze their associations with oral microorganisms.

A total of 423 volunteers were assigned into two cohorts. Paired saliva samples were collected from cohort 1 (n = 60) and underwent metabolomics analysis before and after filtration. SRMs were identified based on the following thresholds: variable importance in projection ≥1, false discovery rate <0.05, and fold change ≥10. The pre-filtration samples from Cohort 1 were subjected to microbiome analysis. Saliva samples collected from cohort 2 (n = 334) underwent metabolomic and microbiome analyses, but were not filtered.

Principal coordinates analysis revealed a clear separation between pre- and post-filtration samples. The filtered saliva samples had approximately 5.8% fewer detectable metabolites. Notably, over half of the SRMs had an unknown origin, indicating significant knowledge gaps in oral metabolites. Prevotella melaninogenica and Veillonella parvula were core species associated with the SRMs (hypoxanthine and phosphatidylcholine), with purine metabolism identified as enriched pathway for Prevotella melaninogenica.

Filtration can reshape saliva metabolite profiles. This study combined key metabolite filtration with integrated multi-omics and functional analyses, providing new insights into saliva metabolism and microbe-metabolite interactions.