Fig. 3

Identification of differentially associating taxonomic features that are diagnostic of the three different groups (Controls, CD and ITB). A Identification of the most diagnostic features for each pairwise group classification, using multiple Random Forest models each considering only a varying number of top features (e.g. top 10, 20, 30, 40, till 250). For each pair of groups (Controls vs. CD, Controls vs. ITB, CD vs. ITB), the most diagnostic set of features were the ones corresponding to the model with the highest classification AUC. B Boxplots comparing the AUC ranges for the 50 iterative bootstrapped Random Forest (RF) model variants. As shown, the variants were generated for discriminating between each pair of groups (Controls vs. CD, Controls vs. ITB, CD vs. ITB), each considering only the top features identified (in A) for corresponding group-pair. For a given pair of groups, to create the RF variant in each iteration we randomly selected 50% of the samples (for generating the training RF model). This model was then tested on the rest 50% of the samples (corresponding to the concerned pair of groups). C–D Heatmaps showing the cross-group variation of the different taxonomic features identified in A to be amongst the top features discriminating across at least one pair of groups at the microbiome (i.e. Bacteriome/Archaeome) (C) and the mycobiome level (D). The upper heatmap groups these features based on their differential abundance/detection across each of the subject group pairs (Controls, ITB vs. Controls, ITB vs. CD; indicated by green color in the lower heatmap). In this scenario, for any pair in the notation ‘A vs. B’, the taxonomic features increased (in abundance or detection) in A with respect to B are highlighted in different shades of pink (FDR < =0.1) and those that are decreased are denoted in different shades of blue as denoted by the key. Markers that enable discrimination between controls vs. ITB/CD are highlighted in boxes with yellow boundaries, while those that facilitate distinguishing between ITB and CD are shown in boxes with blue lines. Abundance of features are denoted in blue font and detection are denoted in blue fonts