Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the 
gastrointestinal tract of uncertain origin, which includes ulcerative colitis 
(UC) and Crohn's disease (CD). The composition of gut microbiota may change in 
IBD affected individuals, but whether dysbiosis is the cause or the consequence 
of inflammatory processes in the intestinal tissue is still unclear. Here, the 
composition of the microbiota and the metabolites in stool of 183 subjects (82 
UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and 
the microbiological profiles were significantly different between IBD and 
healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, 
and Fusobacteria were significantly increased, whereas Bacteroidetes and 
Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, 
Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, 
Flavobacterium, and Oscillospira decreased. Various metabolites including 
biogenic amines, amino acids, lipids, were significantly increased in IBD, while 
others, such as two B group vitamins, were decreased in IBD compared to healthy 
subjects. This study underlines the potential role of an inter-omics approach in 
understanding the metabolic pathways involved in IBD. The combined evaluation of 
metabolites and fecal microbiome can be useful to discriminate between healthy 
subjects and patients with IBD.