Bioinformatics-driven salivary microbial and functional profiling for identifying biomarkers in oral cancer and tobacco abusers in the Indian population

Abstract

Objective

To investigate alterations in the salivary microbiome and its functional potential in Oral Squamous Cell Carcinoma (OSCC) patients, tobacco abusers, and healthy individuals in order to identify microbial biomarkers and gain insight into OSCC pathogenesis.

Design

Saliva-derived 16S rRNA gene sequences from OSCC patients, tobacco users, and healthy controls were obtained from the Indian Biological Data Centre (IBDC). Taxonomic classification was performed using QIIME2, and functional prediction was conducted with MicFunPred. Alpha and beta diversity, differential abundance, and pathway enrichment analyses were used to compare microbial communities and functions among the groups.

Results

OSCC samples showed significantly reduced alpha diversity and distinct microbial community profiles relative to healthy controls. Genera including Porphyromonas, Streptococcus, Rothia, and Parvimonas were enriched in OSCC and are associated with inflammation and carcinogenesis. Tobacco users exhibited increased microbial richness, with dominance of Prevotella, Veillonella, and Peptostreptococcus, indicative of adaptation to chemical exposure. Functional predictions in OSCC samples indicated enrichment in pathways related to bacterial chemotaxis, lipopolysaccharide biosynthesis, glycolysis, and DNA repair. Tobacco-associated microbiota showed elevated oxidative stress response and detoxification pathways.

Conclusions

Microbial dysbiosis and functional alterations in the oral microbiome are strongly associated with OSCC and tobacco use. The identification of disease-specific microbial signatures and pathways highlights the potential of the oral microbiome as a non-invasive biomarker and therapeutic target for precision medicine in OSCC, particularly in the Indian population.