Salivary prognostic bacterial signatures associated with survival outcomes and recurrence risk in head and neck squamous cell carcinoma

Background Alterations in the oral microbiota are increasingly recognized as an integral component of the tumor microenvironment, forming a clinically relevant oncobiome that may modulate tumorigenesis, therapeutic response, and patient prognosis in head and neck squamous cell carcinoma (HNSCC). Methods In this prospective study, we characterized the salivary microbiome of 124 Spanish HNSCC patients (86 laryngeal and 38 pharyngeal carcinomas) and 66 healthy controls from northern Spain using 16S rRNA gene sequencing. Microbial community structure, differential abundance, and associations with tumor site and treatment received were analyzed using ANCOM-BC, while prognostic associations were assessed through univariable and multivariable Cox regression models and survival analyses. Results Distinct microbial community profiles were observed between patients and controls, revealing pronounced site-specific dysbiosis between pharyngeal and laryngeal tumors. Microbiome composition also varied according to treatment modality. Chemoradiotherapy induced a marked remodeling of the oncobiome, characterized by a post-treatment enrichment of Lactobacillus . More importantly, a specific 10-bacteria salivary signature was significantly associated with poorer survival outcomes. including disease-specific survival (DSS), overall survival (OS), and disease-free survival (DFS). This 10-bacterial signature remained independently associated with poor prognosis in multivariable analysis for DSS (HR = 6.215; p < 0.001), OS (HR = 5.417; p < 0.001), and DFS (HR = 6.842; p < 0.001), after adjustment for established clinicopathological variables. Furthermore, we identified tumor site–specific prognostic taxa within the oral microbiome of HNSCC patients. The presence of putative Prevotella , Porphyromonas and Fusobacterium species specifically and significantly correlated with improved DSS, OS and DFS in pharyngeal carcinomas, whereas putative Stomatobaculum longum and Dialister were associated with favorable survival outcomes in laryngeal carcinomas. Conclusions Our findings reveal distinct oral microbial patterns linked to HNSCC prognosis and recurrence risk, demonstrating that the salivary microbiome may represent a source of non-invasive, dynamic biomarkers for risk stratification and personalized management. The identification of tumor site–specific bacterial signatures associated with both favorable and unfavorable survival outcomes supports the concept of an anatomically contextualized oncobiome, although validation in independent cohorts and higher-resolution microbiome studies will be required before clinical implementation.