Fig. 9: Analysis of the microbial composition in the colon.

Faecal matter was taken from the colon of naïve mice (n = 3), severe arthritis (CIA high, n = 3, disease scores 11, 10 and 7), mild arthritis (CIA low, n = 3; disease scores 3, 4 and 4), symptomatic OIT mice (OIT high, n = 3; disease scores 5, 6 and 4) and asymptomatic OIT mice (OIT low, n = 3) at day 33, when DNA was isolated and subjected to 16 S ribosomal RNA (rRNA) amplification and sequencing. a Alpha Diversity analysis, including observed_ otus, shannon, simpson, chao1, dominance and pielou_e indices. Each dot represents one individual mouse; graphs show the mean ± SEM. Kruskal–Wallis test was used to analyze whether the differences in species diversity between groups were significant, *p < 0.05. b Beta diversity indices heatmap of unweighted unifrac distance Matrix. The size and colour of the circle in the square represent the differences in coefficient between the two samples. The larger the circle is, the darker the corresponding colour is, indicating that the differences between the two samples are greater. c Relative abundance of the indicated phyla. Each column shows data from individual mice. Data are also presented as pie charts, presenting proportion values for each group as means. d Clustering of species abundance. The top 35 genera in abundance were clustered from the species and sample levels according to their abundance information in each sample. Heatmap in grey scale shows the mean value of all mice in the group for Z value of taxonomic relative abundance after standardisation. The coloured heatmap represents the values for individual mice: the x-axis represents the sample name, and the y-axis represents the function annotation. The cluster tree on the left side is the species cluster tree. e Relative abundance of the indicated genera. Data show mean ± SEM and dots represent individual mice.