Table 3 Overview of human studies that demonstrate an association between IBD and compositional dysbiosis of the intestinal microbiota determined with culture-independent methods Conventional culturing Swidsinski et al. (2002) 218 Faeces Faeces Study material Biopsies (terminal ileum, colon) Biopsies: inﬂamed and non-inﬂamed tissue (ileum, ascending/sigmoid colon) Colonic biopsies: inﬂamed tissue Rectal biopsies: inﬂamed and non-inﬂamed tissue Biopsies: inﬂamed and non-inﬂamed tissue (ileum, ascending/sigmoid colon) Biopsies: inﬂamed and non-inﬂamed tissue (ileum, ascending/transverse/ descending colon, rectum) Biopsies: inﬂamed and non-inﬂamed tissue (ileum, transverse/sigmoid colon, rectum) Faeces Biopsies: inﬂamed and non-inﬂamed tissue (ileum, ascending/transverse/ descending/sigmoid colon, rectum) Faeces (several time points) 123 Analytical methods Dot-blot hybridisation TGGE Clone library sequencing (16S) Clone library sequencing (16S) Population 12 CD patients (active disease) 12 UC patients (active disease) 14 Non-IBD controls 28 Self-limiting colitis patients 104 Indeterminate colitis patients 119 UC patients 54 CD patients 40 Non-IBD controls 8 CD patients (active disease) 9 CD patients (in remission) 16 Healthy individuals 4 CD patients 4 Healthy controls 26 CD patients (active disease) 31 UC patients (active disease) 15 Inﬂammatory controls 31 Non-inﬂammatory controls 4 CD patients (active disease) 2 CD patients (in remission) 14 UC patients (active disease) 19 UC patients (in remission) 14 Non-IBD controls 20 CD patients 20 UC patients 20 Self-limiting colitis patients 20 IBS patients 20 Non-IBD controls 20 CD patients (active disease) 15 UC patients (active disease) 14 Non-IBD controls 6 CD patients 5 UC patients 5 Non-IBD controls 6 CD patients (in remission) 6 Healthy individuals 19 CD patients 2 UC patients 1 Ischemic colitis patient 15 Non-IBD controls 16 CD patients 18 Healthy individuals FISH qPCR FISH SSCP qPCR FISH FISH Genes Nutr (2011) 6:209–240 References Kleessen et al. (2002) Seksik et al. (2003) Mangin et al. (2004) Ott et al. (2004) Mylonaki et al. (2005) Swidsinski et al. (2005) Bibiloni et al. (2006) Gophna et al. (2006) Manichanh et al. (2006)* Martinez–Medina et al. (2006) Clone library sequencing (16S) DGGE qPCR Clone library sequencing (16S) Clone library screening (metagenome: 16S) FISH/ﬂow cytometry DGGE 16S rRNA gene sequence analysis DGGE Scanlan et al. (2006)