Fig. 4

Nested 16S rRNA gene amplification and sequencing approach for tissue, paraffin and controls. The 16S rRNA amplicon sequencing results of formalin-fixed paraffin embedded (FFPE) tissue (n = 38), empty paraffin controls (n = 21), DNA extraction controls (n = 6), polymerase chain reaction (PCR) negatives (n = 2) and synthetic mock communities (n = 2) at genus level using a nested PCR approach. a Dot plots show the bacterial biodiversity measured by Shannon and Chao1 diversity indices. b Principal Coordinates Analysis (PCoA) plots illustrate the bacterial composition of tissue, paraffin and the different controls using weighted UniFrac and Bray-Curtis dissimilarity. c Heat map analysis of the relative abundance of genera across samples. Tissue specimens consist of tumor (n = 11), normal adjacent tissue (n = 14) and healthy colonic tissue (n = 13). The red box indicates the genera present in PCR negatives and other samples. The red dotted line separates the DNA extraction negatives that were processed separately during library preparation. Abbreviations for level of significance: n.s. not significant; #, P < 0.1; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001