biostudies-literatureZhang FHong Kong Research Grants Council (RGC) General Research Fund (GRF)Federal Government through the St George and Sutherland Medical Research FoundationHong Kong Innovation and Technology Fund (ITF)53https://www.ebi.ac.uk/biostudies/studies/S-EPMC9866815biostudies-literatureUnknown15(1)Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major diversity patterns of alpha and beta diversities and identify the altered viral profiles in the HCC stool samples compared with healthy controls. Viral sigVirusesCritical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients.PMC986681511206819MRP/071/20XZhang FChen GGia AJiang XTGong LBehary JZekry AHold GLSun YTang XEl-Omar EfalseCritical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients.Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major diversity patterns of alpha and beta diversities and identify the altered viral profiles in the HCC stool samples compared with healthy controls. Viral sig2022-01-01T00:00:00Z2022 Dec2026-04-08T12:03:11.05Z2024-11-09T20:44:38.916ZS-EPMC98668153668009410.3390/v15010053