Fig. 1

Tumor microbiomes were closely associated with changes in host metabolism and epigenetic and gene expression profiles. a Shannon index of the microbiota of samples from tumor tissues and normal control liver tissues. The vertical axis represents the α diversity of the microflora. Different colors represent different groups of samples. b PCA scatter plots of microbiota between tissue samples. c The top 20 microbial taxa with significant differences in relative abundance between HCC tissues and healthy tissues. d PCA scatter plots of metabolomes between tissue samples (*p < 0.05; **p < 0.01). e Differential metabolites from cancer tissues and adjacent tissues were identified based on heatmap analysis of Euclidean hierarchical clustering. The horizontal axis represents the different metabolites, the vertical axis represents the samples of different groups, and the red and blue colors represent an increase and a decrease in metabolism, respectively. f PCA scatter plots of transcriptomes between tissue samples. g Volcano plot of the DEGs in the HCC and paired samples. The abscissa represents the log2FoldChange of gene expression between different groups. The ordinate represents the significance level of the expression difference. h Differential gene genome circle diagram. The outermost circle is the chromosome band, the innermost circle is the histogram of the log2FoldChange value of the DEGs, and the middle two circles are the log2(FPKM + 1) distribution diagrams of the two groups of genes. i GSEA of DEGs was significantly correlated with cell cycle, cell cycle process, nuclear chromosome, protein-DNA complex, transcription regulatory region, and sequence-specific DNA binding pathway. j PCA scatter plots of genes DNA methylation between tissue samples. k Volcano plot of the different methylation genes in the HCC and paired samples. The abscissa represents the log2FoldChange of gene expression between different groups. The ordinate represents the significance level of the expression difference. Red dots represent hypermethylation. Green dots represent hypomethylation. Gray dots represent that the difference in methylation was not statistically significant. l Venn diagram of gene data showing opposite trends of DNA methylation in promoter regions and corresponding gene expression levels. m Heatmap of DNA methylation-related differential genes. n Correlation between different bacterial classes and the 24 most abundant metabolites in HCC tissues and healthy liver tissues. o Spearman correlation analysis between the microbiome and DNA methylation-related differential genes. Abbreviation: PCA principal component analysis. HCC hepatocellular carcinoma; DEGs differentially expressed genes; FPKM Fragments Per Kilobase per Million