Abstract Objective: Alterations in microbiome have been linked to Oral squamous cell carcinoma (OSCC) by few earlier studies. We aimed to assess such changes in OSCC patients. Methods: 16S rRNA metagenomic analysis of saliva samples from OSCC patients and health were performed by the latest next generation sequencing (MinION nanopore platform) using pan-eubacterial primers that amplify the entire 16S rRNA gene. The sequences were analysed with MG-RAST. Results: Capnophilic Capnocytophaga species, (Capnocytophaga gingivalis Capnocytophaga ochracea, Capnocytophaga sputigena, Capnocytophaga cynodegmi and Capnocytophaga canimorsus) were found to be in low abundance among OSCC patients compared to the healthy subjects. Conclusion: These findings suggest the association of Capnocytophaga species to health.