Propolis altered the composition of the intestinal microbiota in colitis rats. Rats’ caecal digesta from untreated control, 0% propolis and 0.3% propolis groups were collected and the intestinal microbiota were examined by 16S rRNA sequencing. (a) Alpha diversity was analysed by Shannon diversity index; Data are presented as box plots, n = 8 rats/group; * p < 0.05, and ** p < 0.01 significant difference among two groups; (b) Beta diversity between the groups was analysed by weighted UniFrac distance. Data are the mean ± SEM (n = 8). *** p < 0.001 significant difference among two groups; (c) PCoA plot of the gut microbiota based on an unweighted UniFrac metric; (d) Venn diagram of OTUs showed microbiota differences between untreated control (green area) and 0% propolis (red area) and between 0.3% propolis (blue area), showing strains altered in these groups, and the overlap among them; and (e) relative abundance of predominant bacteria at the phylum level. Data are presented as a staked bar chart, n = 8 per group.