Inclusion Criteria:  Signed informed consent Diagnosis of microscopic colitis (collagenous or lymphocytic colitis) Active disease with no medication (e.g. budesonide) or stable budesonide treatment with or without symptoms Age between 18-75  Exclusion Criteria:  Previous diagnosis of other organic gastrointestinal disease that interferes with the outcome parameters used in this study (e.g. ulcerative colitis) Previous abdominal surgery which might influence gastrointestinal function, except appendectomy and cholecystectomy History of or present gastrointestinal malignancy or polyposis Diagnosis of gastrointestinal infection within the last 6 months Current diagnosis of dementia, severe depression, major psychiatric disorder, or other incapacity for adequate cooperation Chronic neurological/neurodegenerative disease (e.g. Parkinson's disease) Autoimmune disease (e.g. rheumatoid arthritis) Chronic pain syndromes (e.g. fibromyalgia) Chronic fatigue syndrome Severe endometriosis Coeliac disease Diagnosis of lactose intolerance within the last 3 months Pregnancy or breast-feeding Regular intake of anti-inflammatory and/or other immunosuppressive medication than budesonide within the last 3 months Intake of proton pump inhibitors (e.g. omeprazol) within the last 4 weeks Use of anti-depressants within the last 3 months Regular intake of mast cell stabilizing drugs (e.g. sodium cromoglycate) within the last 3 months Antimicrobial treatment within the last 12 weeks before baseline sampling Antimicrobial prophylaxis (e.g. urinary tract infection) Regular intake of probiotics, nutritional supplements, or herb products that might affect intestinal function within the last 4 weeks if the investigator considers that those could affect study outcome Inability to maintain current diet and lifestyle during the study period Alcohol or drug abuse Any clinically significant present or past disease/condition which the investigator considers to possibly interfere with the study outcome