26 Coeliac patients (no diet, active disease) 23 Children without gluten intolerance 20 Coeliac patients (no diet, active disease) 10 Coeliac patients (gluten-free diet, symptom-free) 8 Children without gluten intolerance 10 Coeliac patients (no diet, active disease) 10 Children without gluten intolerance 30 Coeliac patients (no diet) 18 Coeliac patients (gluten-free diet) 30 Children without gluten intolerance 24 Coeliac patients (no diet, active disease) 18 Coeliac patients (gluten-free diet, symptom-free) 20 Children without gluten intolerance 20 Coeliac patients (active disease/ symptom-free) 10 Children without gluten intolerance 18 Patients with polyps 32 Individuals with high -risk for colon cancer 38 Individuals with low-risk for colon cancer 13 Patients at high risk for sigmoid colon cancer 14 Healthy individuals 20 Colon cancer patients 20 Polypectomized patients 20 Healthy individuals 21 Individuals with adenomas 23 Individuals without adenomas 12 Patients with pouchitis 14 Patients with indeterminable pouchitis 23 Patients without pouchitis 20 Ileostomy patients 9 Healthy individuals 5 Patients with pouchitis 9 Patients without pouchitis UC patients: 8 Patients with healthy pouches 9 Patients, no active pouchitis for at least 1 year 9 Patients, no active pouchitis for at least 6 weeks 11 Patients with pouchitis, on antibiotic treatment 8 Patients with pouchitis FAP patients: 5 Patients with healthy pouches Conventional culturing FISH FISH/ﬂow cytometry DGGE qPCR TGGE DGGE Table 5 Overview of human studies that demonstrate an association between intestinal disease and compositional dysbiosis of the intestinal microbiota Population Analytical methods Reference 224 Study material Coeliac disease Faeces Duodenal biopsies Faeces Faeces Duodenal biopsies faeces Duodenal biopsies Colorectal cancer Faeces Faeces Faeces (3 time points) Colorectal biopsies Pouchitis Pouch biopsies Ileostomy efﬂuent Faeces Pouch efﬂuent Pouch efﬂuent 123 Genes Nutr (2011) 6:209–240 Collado et al. (2007) Nadal et al. (2007) Sanz et al. (2007) Collado et al. (2008a) Schippa et al. (2010) Scanlan et al. (2008) Shen et al. (2010) FISH/ﬂow cytometry De Palma et al. (2010) Conventional culturing Conventional culturing Ruseler-van Embden et al. (1994) Ohge et al. (2005) Conventional culturing Moore and Moore (1995) Conventional culturing Kanazawa et al. (1996) T-RFLP Clone library sequencing (16S) FISH Conventional culturing Onderdonk et al. (1992)