Comprehensive analysis of the gastric metatranscriptome reveals specific viral signatures associated with gastric cancer.

Gastric cancer (GC) remains highly lethal, and although gastric microbiome dysbiosis has been linked to carcinogenesis, the viral component is still poorly explored. Here, we used metatranscriptomics to characterize the gastric virome and evaluate its association with GC and clinicopathological features. We analyzed 238 gastric tissues (214 GC and 24 non-tumors, NT) with clinicopathological data. Viral classification was performed using Kraken2 with the RVDB database. Virome diversity, composition, and clustering were assessed using phyloseq-based analyses, Jensen-Shannon divergence with PAM clustering, and ordination methods. Differential abundance and diversity were evaluated using LEfSe and statistical tests, and viral gene expression was investigated for clinical relevant viruses. We identified 106 viral genera, predominantly bacteriophages and dsDNA viruses, with distinct GC- and NT-associated viral signatures. Clustering revealed three viral community types (GT-1, GT-2, GT-3) that significantly separated GC and NT samples and showed reduced alpha diversity in GC-associated clusters. GT-1 was dominated by Lymphocryptovirus, GT-2 by Gorganvirus, and GT-3 (NT) exhibited the highest diversity. GC tissues were enriched in oncologically relevant viruses, including Lymphocryptovirus (EBV), Cytomegalovirus, and Alphapapillomavirus, whereas several bacteriophages predominated in NT. Virome composition was significantly associated with Lauren histological subtype, but not with clinical stage, tumor location, or neoadjuvant therapy. EBV-high tumors displayed a predominantly latent transcriptional program, with strong expression of ncRNAs (RPMS1, EBERs) and low lytic activity. These findings highlight major virome restructuring in GC and support a potential role of the gastric virome in tumor-associated microbial ecology, warranting further mechanistic and clinical investigation.