Samples marked with “”I”" are from inflamed intestinal regions, those marked with “”N”" are from non-inflamed

regions. Non-IBD control samples are indicated with N1-N5. Adjacent bar charts show the Family level classification (as determined by the RDP classifier) for each of the sequences per sample. Families coloured in yellow/brown belong to the Firmicutes phylum, blue = Bacteroidetes, pink = Actinobacteria, green = Proteobacteria, black = all other sequences not belonging to the specified Families. Figure 5 Principal coordinates analysis of variation between the bacterial communities present in all biopsy samples. Each data point

Cediranib concentration represents an individual sample. Blue circles Ganetespib denote non-IBD control samples, red squares are Crohn’s disease samples, green triangles are ulcerative colitis samples. Numbers indicate the donor the samples were obtained from. The paired, inflamed and non-inflamed, biopsy samples from each donor can be seen to cluster together. Figure was calculated using unweighted Fast UniFrac [39]. Statistical comparisons between inflamed and non-inflamed tissue We therefore sought to properly determine whether or not a characteristic localised dysbiosis between healthy and inflamed tissue within individual

IBD patients exists. To test this we first performed whole community comparisons using ∫-LIBSHUFF [38], unweighted and weighted UniFrac [39] and the selleck chemicals parsimony P-test [40] which all test whether or not two communities Ribociclib in vitro are significantly different overall without indicating which phylotypes cause the significance. We then used the Library Compare tool at the RDPII website [41], which pinpoints significant differences between two communities at all taxonomic designations from phylum to genus level to try and discover which bacterial groups were differentially abundant between the paired samples. Analyses with these tools indicated that in 11 out of the 12 IBD patients robust statistically significant differences between the inflamed and non-inflamed mucosal communities existed (Table 2). Table 2 Comparison of bacterial composition from inflamed and non-inflamed tissue within individual IBD patients using ∫-LIBSHUFF, unweighted and weighted UniFrac, the parsimony P-test and RDP Library Compare.