Figure 3.

[A] Alpha-diversity of the luminal and mucosa-associated microbiota. Shannon an effective number of species. Sample locations and genotypes are indicated. [B–D] Multidimensional scaling [MDS] plots of microbial profiles of faecal, ileal and colonic samples stratified by genotype, respectively. [E] Phylogenetic tree showing the similarities between microbiota profiles based on generalized UniFrac distances in luminal [n = 61] and mucosa-associated microbiota [n = 166] derived from 23 pigs [seven wild-type, 16 TNF^ΔARE]. Individual taxonomic composition at the phylum level is shown as stacked bar plots around the phylogram. Innermost ring shows stratification based on sample type, upper GI tract samples [blue] and lower GI tract and stool samples [brown] and denoted by an asterisk [*]; the second ring shows stratification based on genotype, wild-type [grey], TNF^ΔARE/+ [pink] and TNF^ΔARE/ΔARE [green] and denoted by two asterisks [**]. Bars in the outer ring of the figure indicate samples derived from each pig and denoted by three asterisks [***]. [F–H] Taxonomic composition at the phylum level in faecal, ileal and colonic samples stratified by genotype. [I] Phylogenetic tree showing the similarities between microbiota profiles based on generalized UniFrac distances in luminal microbiota derived from wild-type and TNF^ΔARE pigs and mice. Individual taxonomic composition at the phylum level is shown as stacked bar plots around the phylogram. Innermost ring shows stratification based on species, mouse or pig; and the outer ring shows stratification based on genotype, wild-type [grey], TNF^ΔARE/+ [pink] and TNF^ΔARE/ΔARE [green]. [J] Alpha-diversity of luminal microbiota from wild-type and TNF^ΔARE pigs and mice is shown as Shannon effective number of species. [K] MDS plot of microbial profiles of faecal samples stratified by species [mouse or pig] and genotype, respectively. [L] Alpha-diversity of luminal and mucosal microbiota from human IBD patients and wild-type and TNF^ΔARE pigs is shown as Shannon effective number of species. [M] MDS plot of microbial profiles of samples stratified by species [human or pig] and disease activity or genotype, respectively.