Klebsiella variicola in family Enterobacteriaceae is exclusively isolated from the MAT of CD patients. A,B) A pie chart illustrating the number of isolates belonging to each bacterial family in MAT of CD patients and the non‐CD control. C) The specific species in the family Enterobacteriaceae. D) Cultivable bacteria recovered from MAT of CD and non‐CD (at the genus level). In each group, bacteria isolated from more than one specimen are shown. Each column represents the cultivable bacteria community in an individual patient. Members belonging to the family Enterobacteriaceae are shaded black, while members exclusively isolated from CD MAT are shaded red. E) Detection of Klebsiella spp. in MAT from CD patients and the non‐CD controls by fluorescence in situ hybridization (FISH). Sections of MAT were stained with DAPI (blue), Klebsiella spp. (green), (scale bar = 10 µm). F) Four strains of K. variicola (K. variicola ZSLY01, K. variicola ZSLY02, K. variicola ZSLY03, K. variicola ZSLY04) elicit inflammatory responses toward IEC‐6 (rat intestinal epithelial cells) (Unpaired Student's t‐test). G) Phylogenetic analysis by maximum likelihood for identification of the isolated Klebsiella spp., based on conserved functional genes derived from whole‐genome sequencing. (H&I) The distribution of Klebsiella spp. and K. variicola in the gut microbiome of patients with CD using published data (publicly available database (PRJEB15371) (Mann–Whitney U‐test). *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.