The intestinal microbiome is dysregulated in inflammatory bowel disease (IBD), with significant changes in microbial function and metabolism. This study analyzed the microbiota of 231 IBD and healthy subjects using 16S gene pyrosequencing and shotgun metagenomics. The results showed that microbial function was more consistently perturbed than composition, with 12% of analyzed pathways changed compared to 2% of genera. Major shifts in oxidative stress pathways, decreased carbohydrate metabolism and amino acid biosynthesis, and increased nutrient transport and uptake were observed. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. The study also identified significant associations between microbiome composition and host factors such as treatment, age, and smoking. The microbiome of IBD patients showed distinct patterns, with reduced abundance of certain clades like Roseburia and Faecalibacterium in ileal Crohn's disease, and increased abundance of Enterobacteriaceae in CD. The study highlights the importance of microbial metabolism in IBD pathogenesis and the need for further research into the functional roles of the microbiome in IBD. The findings suggest that the microbiome plays a crucial role in maintaining gut homeostasis and that dysbiosis in IBD is associated with major impairments in microbial metabolic functions. The study provides insights into the functional metagenomic information that underpins IBD pathogenesis.The intestinal microbiome is dysregulated in inflammatory bowel disease (IBD), with significant changes in microbial function and metabolism. This study analyzed the microbiota of 231 IBD and healthy subjects using 16S gene pyrosequencing and shotgun metagenomics. The results showed that microbial function was more consistently perturbed than composition, with 12% of analyzed pathways changed compared to 2% of genera. Major shifts in oxidative stress pathways, decreased carbohydrate metabolism and amino acid biosynthesis, and increased nutrient transport and uptake were observed. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. The study also identified significant associations between microbiome composition and host factors such as treatment, age, and smoking. The microbiome of IBD patients showed distinct patterns, with reduced abundance of certain clades like Roseburia and Faecalibacterium in ileal Crohn's disease, and increased abundance of Enterobacteriaceae in CD. The study highlights the importance of microbial metabolism in IBD pathogenesis and the need for further research into the functional roles of the microbiome in IBD. The findings suggest that the microbiome plays a crucial role in maintaining gut homeostasis and that dysbiosis in IBD is associated with major impairments in microbial metabolic functions. The study provides insights into the functional metagenomic information that underpins IBD pathogenesis.