This study investigates the functional dysfunctions of the intestinal microbiome in inflammatory bowel diseases (IBD), specifically Crohn's disease (CD) and ulcerative colitis (UC). The researchers analyzed microbial communities from 231 IBD patients and healthy controls using 16S gene pyrosequencing and shotgun metagenomics. They found that while Firmicutes and Enterobacteriaceae abundances were associated with disease status, microbial function was more consistently perturbed than composition. The study identified significant shifts in oxidative stress pathways, decreased carbohydrate metabolism, and amino acid biosynthesis, with a shift towards nutrient transport and uptake. Notably, ileal CD (iCD) showed increases in virulence and secretion pathways. The findings provide insights into the community-wide microbial processes and pathways underlying IBD pathogenesis, highlighting the importance of functional metagenomic analysis in understanding the complex interactions between the gut microbiome and IBD.This study investigates the functional dysfunctions of the intestinal microbiome in inflammatory bowel diseases (IBD), specifically Crohn's disease (CD) and ulcerative colitis (UC). The researchers analyzed microbial communities from 231 IBD patients and healthy controls using 16S gene pyrosequencing and shotgun metagenomics. They found that while Firmicutes and Enterobacteriaceae abundances were associated with disease status, microbial function was more consistently perturbed than composition. The study identified significant shifts in oxidative stress pathways, decreased carbohydrate metabolism, and amino acid biosynthesis, with a shift towards nutrient transport and uptake. Notably, ileal CD (iCD) showed increases in virulence and secretion pathways. The findings provide insights into the community-wide microbial processes and pathways underlying IBD pathogenesis, highlighting the importance of functional metagenomic analysis in understanding the complex interactions between the gut microbiome and IBD.