Characterization of the gut virome in patients with nonalcoholic fatty liver disease

Nonalcoholic fatty liver disease (NAFLD) is a prevalent metabolic disorder with complex gut microbiome involvement. While bacterial dysbiosis in NAFLD has been widely studied, the role of the gut virome remains largely unexplored. We profiled gut viral communities from 90 NAFLD patients and 90 non-NAFLD controls using whole-metagenome shotgun sequencing. Viral taxonomic composition, host associations, and functional gene repertoires were analyzed. Serum metabolomic data were integrated to assess virus–metabolite interactions, and random forest models were constructed to evaluate the diagnostic potential of viral signatures. Overall viral diversity showed no significant differences between NAFLD and controls, but subtle compositional shifts were detected at the vOTU level, with 105 viruses enriched in NAFLD and 185 in non-NAFLD individuals. NAFLD-enriched phages primarily targeted Bacteroides, whereas non-NAFLD-enriched phages were associated with beneficial genera such as Faecalibacterium, Oscillibacter, and Prevotella. Functional annotation revealed a reorganization of viral gene repertoires: genes involved in DNA recombination and horizontal transfer (e.g. int, recD) were depleted, while those related to host interaction and stress response (e.g. xerD, dnaK, hipB) were enriched in NAFLD, indicating enhanced viral persistence and host communication. Serum metabolomic profiling identified 8 differential metabolites, and correlation analysis linked specific vOTUs with altered metabolic pathways. A random forest model based on viral features achieved an AUC of 0.758, outperforming the bacterial model, while integration of viral and bacterial features further improved prediction (AUC = 0.837). The gut virome in NAFLD undergoes compositional and functional remodeling characterized by a shift toward host-adaptive, metabolically interactive viral communities. These viral alterations are closely associated with host metabolic changes and demonstrate strong diagnostic potential. Our findings highlight the virome as an overlooked yet critical component of the gut ecosystem in NAFLD pathogenesis and as a promising source of noninvasive biomarkers for disease prediction and monitoring.