Metagenomic analysis of tongue samples from healthy subjects identifies distinct microbiome orotypes

Abstract

Abstract Background The tongue dorsum harbors a complex microbiome that remains incompletely characterized. Objective This study aimed to characterize the tongue microbiome—including its phageome—in a healthy Qatari population. Design Shotgun metagenomic sequencing was performed on tongue-coating samples from 92 systemically healthy adults to comprehensively profile the bacteriome, phageome and functional potential of the tongue microbiome. Results Taxonomic profiling revealed a predominantly bacterial community (>99%) dominated by Veillonella, Streptococcus, Neisseria, Rothia, Prevotella, Haemophilus and Pauljensenia. Among low-abundance domains, the fungus Saccharomyces and the protist Entamoeba were most prevalent. Dirichlet–multinomial mixture clustering identified three distinct bacterial ‘orotypes’ (C1–C3) showing significant compositional separation (PERMANOVA, p = 0.001) and alpha diversity differences at both genus and species levels. A major compositional gradient involved enrichment of Neisseria and Haemophilus in C2, their absence in C3 and intermediate representation in C1. Functional profiling revealed a conserved core of housekeeping pathways across orotypes, wherease adaptive functionsdiffered across orotypes, particularly in the Neisseria/Haemophilus-enriched C2 orotype. The phageome was dominated by Uroviricota (class Caudoviricetes). Conclusion The findings identify distinct tongue microbiome orotypes with conserved core functions, divergent taxonomic and metabolic profiles, and provide new insights into the tongue phageome, establishing a foundation for investigating their roles in health.