Immune-mediated inflammatory diseases (IMID) is a term used to define a group of disorders that share common pathogenic mechanisms. IMID include inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus and others. Many studies have linked IMID to dysbiosis (a disruption in the microbiome). Researchers are now investigating whether changes in the gut flora are common between IMID or if specific perturbations are associated with a single disease. A new review explores the current research on the gut microbiota in IMID.