16S rRNA gene libraries were used to compare shifts in bacterial taxon abundance between samples from untreated and DSS-treated mice. All relative abundance shifts stated below are arithmetic averages of replicates and statistically significant (P<0.05). The overall dasatinib IC50 abundances of the dominant phyla Firmicutes (58�C65%) and Bacteroidetes (27�C31%) were not affected by DSS treatment, but taxa within these two phyla showed clear changes in abundance. DSS treatment increased abundance of unclassified Clostridiales (1.8�C4.1%) in mice of both genotypes and of Ruminococcaceae (6�C16%) in STAT1?/? mice (Supplementary Figure S6). The abundance of Bacteroidaceae (1.6�C4.4%) increased but abundances of unclassified Bacteroidales (16.5�C9.6%) and Rikenellaceae (2.7�C1.5%) decreased upon DSS treatment in both genotypes.

The less abundant but consistently detected phyla, Proteobacteria, Verrucomicrobia and Deferribacteres, were each dominated by a single family or genus, Enterobacteriaceae, Akkermansia and Mucispirillum, respectively. Akkermansia increased in DSS-treated mice of both genotypes (ND (not detectable) to 2.2%), whereas Mucispirillum (0.2�C1.6%) and Enterobacteriaceae increased in wt mice only (ND to 4%) (Supplementary Figure S6). To determine if the degree of phylotype kinship influences phylotype dynamics, we compared the Pearson correlation coefficient of phylotype abundance and the genetic distance (that is, 16S rRNA sequence dissimilarity) between all phylotype pairs (using the 16S rRNA gene sequence reads) in control and DSS-treated wt and STAT1?/? mice.

Most phylotype pairs (98.3%) showed no significant correlation. Strong positive and negative correlations were present at varying levels of genetic distance, and there were far fewer strong negative correlations (Figure 2a). The average correlation of phylotypes assigned to the same taxonomic family, which is a measure of the amount of ecological cohesion (Webb et al., 2002), was in all cases positive, but showed substantial diversity (Figure 2b). This diversity was attributable to both the number of phylotypes present in the family (that is, phylotype richness) and average within-family genetic distance. This variation in within-family characteristics was also observed when samples from control mice and DSS-treated mice were considered separately (Figure 2b). Family-level ecological cohesion decreased Drug_discovery with both increasing phylotype richness (R2=0.76) and, to a lesser extent, increasing average within-family genetic distance (R2=0.54) (Supplementary Figure S7). Figure 2 Pearson correlation coefficient of phylotype relative abundance between all phylotype pairs.