Genes Nutr (2011) 6:209–240 Table 3 continued Study material Faeces Faeces Ileal biopsies Biopsies (small intestine and colon) Biopsies (caecum, colon, rectum) Faeces Faeces Faeces (several time points) Colonic biopsies Faeces Rectal biopsies: inﬂamed and non-inﬂamed tissue Faeces Biopsies (terminal ileum, ascending/ transverse/descending colon, rectum) Faeces Population 13 CD patients (active disease) 13 UC patients (active disease) 5 Infectious colitis patients 13 Healthy individuals 29 UC patients (active disease) 12 UC patients (in remission) 46 Healthy individuals 13 CD patients (ileum) 8 CD patients (colon) 7 Non-IBD controls 68 CD patients 61 UC patients 61 Non-IBD controls 13 CD patients 19 UC patients 15 Healthy individuals 17 CD patients (active disease) 17 CD patients (in remission) 20 Healthy controls 10 Twin pairs with CD 8 Healthy twin pairs 16 UC patients (in remission) 8 Healthy controls 15 CD patients (active disease) 8 CD patients (in remission) 44 UC patients (active disease) 29 UC patients (in remission) 9 UC patients (active disease) 11 Non-IBD controls 22 CD patients (active disease) 10 CD patients (in remission) 12 UC patients (active disease) 4 UC patients (in remission) 8 Infectious colitis patients 27 Healthy individuals 10 Twin pairs with CD 8 Healthy twin pairs 6 CD patients (in remission) 6 Healthy individuals Analytical methods FISH/ﬂow cytometry References Sokol et al. (2006)# T-RFLP Andoh et al. (2007) 219 Clone library sequencing (16S) qPCR FISH Clone library sequencing (16S) qPCR RISA Conventional culturing T-RFLP G?C proﬁling Clone library sequencing (16S) T-RFLP DGGE Conventional culturing qPCR FISH HPLC T-RFLP qPCR T-RFLP Clone library sequencing (16S) qPCR qPCR Phylogenetic microarray (16S) Baumgart et al. (2007) Frank et al. (2007) Kotlowski et al. (2007) Andoh et al. (2008) Dicksved et al. (2008) Martinez et al. (2008) Takaishi et al. (2008) Nishikawa et al. (2009) Sokol et al. (2009)# Willing et al. (2009) Kang et al. (2010)* 123