Various studies and trials have indicated a potential link between cancer and the microbiome of the digestive system. Nevertheless, there is insufficient research on the connection between the gut microbiome and Head and Neck Squamous Cell Carcinoma (HNSCC). Genetic differences in the intestinal microbiome were obtained from the MiBioGen repository. We recognized gut microbiota across various taxonomic levels including phylum, class, order, family, and genus. UK Biobank provided the HNSCC data, while the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) database (GSE181919) supplied the HNSCC-related data for single-cell correlation analysis. Following this, we performed Mendelian Randomization (MR), analyzed immune cell infiltration, conducted Gene Set Variation Analysis (GSVA) and Gene Set Enrichment Analysis (GSEA), examined regulatory networks of important genes, conducted single-cell analysis, and performed statistical analysis. Seven ideal causal connections were discovered between the gut microbiome and HNSCC, with their validity confirmed by analyzing heterogeneity and genetic diversity. Examination showed that the Single-nucleotide polymorphism(SNP) genes have a strong connection to levels of immune cell infiltration and are important in shaping the immune microenvironment (IME) . Additional research revealed distinct signaling pathways and transcriptional regulatory networks that were enhanced by the seven SNP genes. Through the use of MR, we were able to establish a direct connection between the gut microbiome and HNSCC. This may contribute to providing new insights into the mechanisms and clinical research of gut microbiota-mediated HNSCC.

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