Fig. 4

Gut microbial functional pathways and functional feature profiles in healthy subjects, patients with CD, and patients with UC. (a–b) PCoA, showing the abundance of functional genes in each sample by groups based on (a) KEGG orthologs (KOs) and (b) enzyme commission categories (ECs) predicted using taxa abundance profiles and genome information. (c–d) Predicted (c) KEGG and (d) MetaCyc metabolic pathways differing significantly in patients with CD and healthy subjects. The FDR values were based on a multivariable generalized linear regression model adjusted for stool consistency, age, sex, body mass index, smoking and alcohol consumptions, and disease activity of IBD. Only significant pathways (FDR < 0.01) are shown. Numerical values indicate coefficients. (e) Heatmap representing KEGG pathways related to sulfur metabolism in patients with CD and healthy subjects, based on significantly different KO abundances in these two groups. Positive z-scores are shown in red color, and negative z-scores are shown in blue. f Volcano plot representing KOs related to sulfur metabolism and sulfur relay system, based on significantly different KO abundances in patients with CD and healthy subjects. KOs related to pathways for producing cysteine ​​from taurine are shown in red, and KOs related to pathways for producing H₂S from cysteine are shown in blue. Statistical significance was determined using PERMANOVA based on 999 permutations (a–b). CD, Crohn’s disease; UC, ulcerative colitis; KEGG, Kyoto Encyclopedia of Genes and Genomes; PCoA, Principal coordinate analysis.