Metagenomic Analysis of the Oral Microbiome in Patients with Head and Neck Squamous Cell Carcinoma: A Case-Control Study

• Niyati V. Thakkar

  Faculty of Allied and Healthcare, Gokul Global University, Sidhpur, Gujarat, India

• Anisha Chaudhary

  Quantum University Research Center, Quantum University, India

• Smiral Gameti

  Faculty of Nursing, Parul University, Vadodara, Gujarat, India

• K. Ezhil Vendhan

  Department of Ophthalmology, Vinayaka Mission’s Kirupananda Variyar Medical College & Hospitals, Vinayaka Mission’s Research Foundation (DU), Salem, Tamil Nadu, India

• Nittin Sharma

  Center for Research Impact & Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University, Rajpura, 140401, Punjab, India

• K.V. Jamuna

  Department of Forensic Science, JAIN (Deemed-to-be University), Bengaluru, Karnataka, India

• Rajesh Kumar Lenka

  Department of Microbiology, IMS and SUM Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India

Head and neck squamous cell carcinoma (HNSCC) is one of the important cancers that are responsible for considerable morbidity all over the world. Recent studies reveal that changes in the oral microbiome are linked with HNSCC, but the exact microbial signatures according to the presence of disease need further research. In this study, metagenomic analysis was done on the oral microbiome of 210 HNSCC patients and 180 healthy controls based on the whole-genome shotgun metagenomic sequencing technique. Microbial diversity analysis, taxonomic profile, functional pathway analysis, and classification using a machine learning algorithm were performed for the identification of HNSCC-specific microbial signatures. HNSCC patients showed considerable changes in oral microbial profile as compared to the healthy subjects. The Shannon diversity index was significantly lower in patients with HNSCC than in control subjects (3.09 ± 0.34 vs 3.82 ± 0.41). An increase in the relative abundance of Fusobacterium, Prevotella, and Porphyromonas was observed in patients with HNSCC, while the relative abundance of the commensal species Streptococcus and Rothia was found to be decreased. The functional annotation revealed enrichment of pathways related to inflammation in the HNSCC samples. Using a random forest approach based on the microbial abundance profile, discrimination was possible between the two groups with a sensitivity of 82%, specificity of 79%, and AUC of 0.86 through cross-validation.

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