The signature of the intrahepatic microbiome in multifocal hepatocellular carcinoma (HCC) and its association with genomic alterations remain elusive. In this study, we performed multiomics profiling of 242 HCC tumor nodules and 58 adjacent nontumor tissues from 58 patients with multifocal HCC, revealing heterogeneous microbial communities in multifocal HCC. The presence of bacteria in HCC nodules was confirmed by Gram stain, lipopolysaccharide, lipoteichoic acid staining, and transmission electron microscopy. Mutational profiling stratified patients into intrahepatic metastasis (IM)–HCC and multicentric occurrence (MO)–HCC. Bacterial communities differed between IM and MO nodules (P = 0.01). A nine-bacterium biomarker panel could distinguish IM nodules from MO nodules with an AUROC of 0.795. The epithelial–mesenchymal transition pathway was upregulated in IM nodules and correlated with IM-enriched bacteria. IM-enriched bacteria such as Enterococcus faecalis and Streptococcus anginosus promoted HCC cell migration, invasion, and tumor progression in orthotopic HCC mouse models by inducing an immunosuppressive microenvironment and epithelial–mesenchymal transition. Collectively, the intrahepatic microbiome contributes to the heterogeneity and pathogenesis of multifocal HCC.

Significance:

We reveal intraindividual heterogeneous microbial communities among nodules from patients with multifocal HCC. IM-HCC–enriched bacteria promote tumor growth and influence the tumor microenvironment of HCC. Our work highlights the necessity of considering bacterial heterogeneity as biomarkers and targets for multifocal HCC therapeutic intervention.

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©2025 The Authors; Published by the American Association for Cancer Research
2025
American Association for Cancer Research
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First page of Intrahepatic Microbial Heterogeneity in Multifocal Hepatocellular Carcinoma and Its Association with Host Genomic and Transcriptomic Alterations<alt-title alt-title-type="short">Intrahepatic Microbiota Contribute to mHCC Heterogeneity</alt-title>

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