A decrease of the butyrate-producing species *Roseburia hominis* and *Faecalibacterium prausnitzii* defines dysbiosis in patients with ulcerative colitis

Bacterial protein signals are associated with Crohn’s disease

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarray

Isolation of *Mycobacterium avium* Subspecies *paratuberculosis* Reactive CD4 T Cells from Intestinal Biopsies of Crohn’s Disease Patients

Mycobacterium avium subspecies paratuberculosis in children with early-onset Crohn’s disease

Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn’s disease

On the prevalence of M. avium subspecies paratuberculosis DNA in the blood of healthy individuals and patients with inflammatory bowel disease

Fungi and inflammatory bowel diseases: Alterations of composition and diversity