Paired biopsy-surface and tissue microbiome profiling reveals tissue-associated bacterial signatures in nasopharyngeal carcinoma

Introduction: Tumor-associated microbiota have been implicated in cancer biology, but the relationship between bacteria detected on the biopsy surface and those detected within tumor tissue remains poorly defined. Methods: In this study, we profiled paired biopsy-surface swabs and tissue biopsies from patients with nasopharyngeal carcinoma (NPC) and benign nasopharyngeal lymphoid hyperplasia (NLH) controls using five-region 16S rRNA gene sequencing. Matched bulk RNA-seq data were analyzed to explore associations between microbial features, Epstein-Barr virus (EBV) transcription, host pathway activity, and inferred immune-cell composition. Results: Tissue-associated microbial profiles showed stronger separation between NPC and NLH than biopsy-surface profiles in this discovery cohort. Several NPC-enriched species-level taxonomic assignments were associated with higher EBV transcript levels, proliferative and cell-cycle pathway activity, and lower inferred CD8 T-cell and plasmacytoid dendritic-cell signatures. Discussion: These findings indicate that NPC tissue contains microbial signatures that differ from biopsy-surface communities and support further validation of tissue-associated microbe-EBV-host relationships.