Fig. 1

The microbiota of inflammatory bowel disease (IBD) patients is taxonomically and functionally divergent from that of healthy donor (HD) subjects. a Linear discriminative analysis (LDA) was performed using linear discriminative analysis effect size (LEfSe) to identify significant differences in relative abundance of various taxonomic groups in the feces of HD subjects compared with ulcerative colitis (UC) patients, or b HD patients compared with Crohn’s disease (CD) patients. Differentially abundant genera for which the corresponding LDA scores indicate P < 0.05 are shown in the graphs. c Distances between the patient groups were calculated using the Bray-Curtis index based on taxonomic data or d Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway data and visualized by principal coordinate analysis. Significant differences between groups were determined by PERMANOVA, and P values are shown at the bottom of the plots. e Copy number of Enterococcus faecium in feces was determined by PCR. *P < 0.05