Characterization of the intrahepatic microbiome in patients with HBV-related end-stage liver disease

Background Dysregulated microbiota is a hallmark of end-stage liver disease (ESLD). This study aimed to elucidate the intrahepatic microbiome in hepatitis B virus (HBV)-related ESLD.Methods We collected liver tissue samples from patients undergoing liver transplantation due to decompensated cirrhosis (DC) (n = 20) or acute-on-chronic liver failure (ACLF) (n = 24), as well as 18 samples from donors. Metatranscriptomic sequencing was performed to profile liver microbiome and transcriptome.Results 2208 bacterial species were detected across 13 phyla and 165 genera. Metatranscriptomic profiling revealed that Proteobacteria and Actinobacteria dominated the intrahepatic microbiome, with Escherichia coli and Pseudomonas most prevalent across groups. Principal coordinate analysis showed distinct microbial community structures among donors, DC, and ACLF patients. Compared with donors, both groups exhibited increased abundance of Bacteroides heparinolyticus, Moraxella osloensis, and Gardnerella vaginalis, while ACLF patients were further enriched with Alcaligenes faecalis and Burkholderia insecticola, and DC patients had higher B. heparinolyticus. Most taxa originated from the gut, with additional oral- and respiratory-derived species. Despite similar abundance between groups, E. coli in ESLD displayed marked functional activation, including nutrient acquisition systems and virulence factors linked to adhesion, invasion, and toxin production. Integrated host – microbiome analysis revealed taxa-specific associations with impaired hepatic metabolic, immune, and structural integrity.Conclusion This study delineates the compositional and functional reprogramming of the intrahepatic microbiome in patients with ESLD and its coupling with liver metabolic, immune, and structural pathways. These findings suggest the intrahepatic microbiome as a promising therapeutic target for ESLD.