Dynamics of tissue and fecal microbiota in active Crohn’s disease and their ability to predict disease state

Figure 1 Comparison between tissue and fecal bacteria in patients with active Crohn’s disease. A and B: Violin plot showing Shannon’s alpha diversity and Faith phylogenetic alpha diversity; C and D: Principal coordinates analyses plots based on weighted Unifrac distances and Bray-Curtis dissimilarity estimates; E: Factors affecting bacterial composition; F: Bacterial genera with significant differences in relative abundance between tissue and stool samples; G: Differentially abundant functional pathways between tissue and stool sample.

Figure 2 Comparison between tissue bacteria in patients with active Crohn’s disease and healthy controls. A and B: Violin plot showing Shannon alpha diversity and Faith phylogenetic alpha diversity; C and D: Principal coordinates analyses plots based on weighted Unifrac distances and Bray-Curtis dissimilarity estimates; E: Factors affecting bacterial composition; F: Presence of dysbiosis based on cloud-based LOcally linear unbiased dysbiosis test; G: Differentially abundant functional pathways between Crohn’s disease and healthy controls.

Figure 3 Comparison between fecal bacteria in patients with active Crohn’s disease and healthy controls. A and B: Violin plot showing Shannon alpha diversity and Faith phylogenetic alpha diversity; C and D: Principal coordinates analyses plots based on weighted Unifrac distances and Bray-Curtis dissimilarity estimates; E: Factors affecting bacterial composition; F: Presence of dysbiosis based on cloud-based LOcally linear unbiased dysbiosis test; G: Differentially abundant functional pathways between Crohn’s disease and healthy controls.

Figure 4 Bacterial genus increased and decreased in stool and tissue samples. A: Bacterial genus increased and decreased in stool samples of patients with active Crohn’s disease compared to healthy controls; B: Bacterial genus increased and decreased in tissue samples of patients with active Crohn’s disease compared to healthy controls.

Figure 5 Bacterial predictors of disease state (active Crohn’s disease and healthy state) in tissue and stool samples. A and B: Random forest analysis showing bacteria predicting active Crohn’s disease and healthy state in tissue sample and stool sample; C: Receiver operating characteristic curve showing ability of top 40 operational taxonomic units in tissue sample selected based on random forest analysis to discriminate between disease and healthy state; D: Receiver operating characteristic curve showing ability of top 65 operational taxonomic units in stool sample to discriminate between disease and healthy state. AUC: Area under curve; CI: Confidence interval.