Characterization of the gut virome in patients with non-alcoholic fatty liver disease

Background: 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. Methods: We conducted a comprehensive analysis of gut viral communities in 90 NAFLD patients and 90 non-NAFLD controls using whole-metagenome shotgun sequencing. Viral taxonomic composition, host associations, and functional gene profiles were characterized. Serum metabolomic data were integrated to explore virus–metabolite interactions, and a random forest model was developed to assess the diagnostic potential of virome signatures. Results: No significant differences were observed in overall viral diversity. However, compositional shifts at the vOTU level revealed 105 viruses enriched in NAFLD and 185 in non-NAFLD individuals. NAFLD-enriched viruses were mainly associated with Bacteroides, while non-NAFLD phages targeted beneficial genera such as Faecalibacterium and Oscillibacter. Functional analysis identified 65 differentially abundant KEGG orthologs, with metabolism-related viral genes notably depleted in NAFLD. Serum metabolomic analysis revealed nine differential metabolites, some of which were significantly correlated with vOTU abundances. A random forest classifier based on viral features achieved an AUC of 75.79% for distinguishing NAFLD status. Conclusion: Our findings demonstrate that the gut virome exhibits compositional and functional alterations in NAFLD, with potential implications for host metabolism. These viral signatures show promise as noninvasive biomarkers and highlight the virome as an overlooked contributor to NAFLD pathogenesis.