Culturomics reveals <i>Fusobacterium</i>-<i>Prevotella</i> mutualism as a hallmark of nasopharyngeal tumor microbiota.

Abstract

The nasopharynx constitutes a critical niche in the upper respiratory tract, harboring a diverse microbiota linked to nasopharyngeal carcinoma (NPC), the mechanistic roles of which remain poorly understood. Here, we established the Nasopharyngeal Mucosal and Tumor-resident Bacterial Catalog (NMTBC) that comprises 5311 bacterial isolates representing 127 species, with 1006 of them being fully sequenced and annotated, providing a comprehensive culturable resource facilitating mechanistic dissection of the microbiome-tumor interactions. With NMTBC, we uncovered a <i>Fusobacterium</i>-<i>Prevotella</i> mutualism and revealed heterotypic bacterium-bacterium interactions involving transcriptional reprogramming and metabolic cross-talk. Using single-bacterial transcriptomics, we mapped a high-resolution transcriptomic trajectory, showing the ability of a single strain to differentiate into functionally distinct subpopulations that cooperate to sustain mutualism. By analyzing a multicenter NPC cohort, we showed that <i>Fusobacterium</i> and <i>Prevotella</i> co-colonization in NPC tumors correlated with unfavorable clinical outcomes after conventional radiochemotherapy. Analysis of RNA-seq data from two previous phase 3 clinical trials showed that coenrichment of <i>Fusobacterium</i>-<i>Prevotella</i> predicted better response to anti-PD-1 immunotherapy, highlighting their important role in microbiota-mediated immunomodulation. Overall, this study establishes a comprehensive nasopharyngeal bacterial catalog through culturomics, which offers valuable insights into microbiome-derived biomarker discovery and immunotherapy patient stratification in clinical practice.