Fig. 5

Differentially abundant pathways and enzyme classes between matched normal and colorectal tissue microbiomes. a Boxplots with corresponding paired dotplots indicating the relative abundances of several pathways showing differential abundance between tumor and normal samples. Lines connect the abundance in the normal (left) and tumor sample (right). Line colors indicate the directionality of the abundance change (blue and red for decreased and increased abundance in the tumor relative to the normal, respectively). Below we plot the difference between the tumor and normal abundance as grey dots, with the purple line representing the 95 % confidence interval (95 % CI) and the mean. Values at 0 (grey dotted lines) represent no change between normal and tumor. b Barchart showing the p values (−log₁₀ transformed) obtained from Fisher’s exact test used to determine virulence category enrichment in the tumor-associated microbiome on the x-axis with the gene categories labeled on the y-axis. Red bars indicate significance by Fisher’s exact test (p < 0.005) and gray bars indicate no statistical significance. The blue dashed line indicates the standard significance cutoff of p = 0.05. c Barchart from the analysis in panel (b), demonstrating the fold-enrichment of virulence protein-encoding genes in the tumor-associated microbiome. The x-axis is the fold enrichment of the different virulence enzyme classes within the tumor microbiome relative to the normal microbiome. The vertical blue dotted line placed at 1 indicates the point where there is no difference between the normal and tumor microbiomes. d Venn diagram indicating the numbers of shared virulence-associated genes among Providencia, Fusobacterium, and the set of statistically significantly increased abundance genes at the tumor