Introduction Inflammatory bowel disease (IBD) is associated with alterations in the interaction between resident microbes and the intestinal immune system. While shifts in microbial populations have been repeatedly shown in studies of the intestinal microbiome from IBD patients, potential confounding factors such as treatment or environmental exposures have not been fully accounted for. Furthermore, the functional implications of these microbial changes have not been determined. Material andMethods The composition of the microbiome from intestinal biopsies and stool samples were analyzed by 16S gene pyrosequencing. Gene and pathway composition were assessed from phylogenetically associated reference genomes. A novel combination of sparse linear modeling and factor analysis was used to associate microbial abundance, genes, metabolic modules, and pathways with disease and with environmental factors such as medications and smoking. Results We analyzed the GI microbiome of 119 patients with Crohn's disease (CD), 74 patients with ulcerative colitis (UC) and 27 healthy subjects (HS). In CD patients, Roseburia and Ruminococcus genus, respectively in the Lachnospiraceae and Ruminococcaceae families in the Firmicutes phylum, were less abundant. In CD patients with ileal involvement (iCD, n=43) specifically, sequences of the Ruminococcaceae family and of the Faecalibacterium genus in particular were reduced compared to other subjects. The only statistically significant feature specific to UC was the overrepresentation of Eggerthella genus (Actinobacteria phylum). Immunosuppressive treatment (azathioprine/6-mercaptopurine or anti-TNF agents) was associated with an increase of Escherichia/Shigella genus (Gammaproteobacteria), whereas mesalamine was associated with a decrease of Gammaproteobacteria. Genes involved in genetic information processing, nucleic acid metabolism and biosynthesis, amino acid metabolism and methane oxidation were significantly less abundant in IBD patients than in HS. Lipid metabolism and catabolism modules were decreased in iCD. Conversely, genes involved in nitrogen and sulfur metabolism, cysteine metabolic process and in some amino acid transport systems (complementing reductions in their metabolism) were overrepresented in IBD. In iCD specifically, genes involved in carbohydrate metabolism, metabolisms of cofactors and vitamins, and virulence factors were more abundant. Conclusion IBD and iCD in particular are associated with a dysbiosis characterized by changes in Firmicutes, Proteobacteria and Actinobacteria phyla. Environmental factors and, importantly, treatments are associated with independent changes in the GI microbiome. These modest perturbations in bacterial composition are in turn associated with major perturbations of GI microbiome function with potential impact on the host.
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