Faeces (2 time points) Faeces Duodenal biopsies Faeces Faeces Faeces (3 time points) Colonic biopsies Faeces Colonic biopsies Faeces Duodenal biopsies Faeces Faeces Faeces Genes Nutr (2011) 6:209–240 Study material Faeces (3 time points) Faeces (3 time points) Biopsies: inﬂamed and non-inﬂamed 20 CD patients tissue (ileum, ascending/sigmoid colon) 20 UC patients 217 Table 2 Overview of human studies that demonstrate an association between IBS and compositional dysbiosis of the intestinal microbiota determined with culture-independent methods Population 27 IBS patients 22 Healthy individuals 26 IBS patients 25 Healthy individuals 20 Self-limiting colitis patients 20 IBS patients 20 Healthy individuals 16 IBS patients 16 Healthy individuals 24 IBS patients 23 Healthy individuals 41 IBS patients 26 Healthy individuals 10 (?2) IBS (only IBS-D) 23 Healthy individuals 20 IBS patients 15 Healthy individuals 10 IBS patients (only IBS-D) 10 Healthy individuals 47 IBS patients 33 Healthy individuals 37 IBS patients 20 Healthy individuals 44 IBS patients 26 IBS patients 26 Healthy individuals Analytical methods qPCR Conventional culturing DGGE Clone library sequencing (16S) FISH References Malinen et al. (2005)* Ma¨tto¨ et al. (2005)* Swidsinski et al. (2005) DGGE TRAC G?C based proﬁling Clone library sequencing (16S) qPCR FISH qPCR G?C based proﬁling Clone library sequencing (16S) qPCR qPCR Conventional culturing qPCR DGGE DGGE Clone library sequencing (16S) qPCR qPCR Conventional culturing qPCR HPLC Maukonen et al. (2006)* Kassinen et al. (2007)* Kerckhoffs et al. (2009)# Krogius–Kurikka et al. (2009)* Lyra et al. (2009)* Carroll et al. (2010) Codling et al. (2010) Kerckhoffs et al. (2010)# Malinen et al. (2010)* Tana et al. (2010) All studies have applied Rome II or III criteria to recruit their subjects and categorise them in IBS subtypes. Studies that have used subjects from the same cohort are indicated by * and # DGGE denaturing gradient gel electrophoresis, FISH ﬂuorescence in situ hybridisation, HPLC high-performance liquid chromatography, qPCR quantitative polymerase chain reaction, TRAC transcript analysis with the aid of afﬁnity capture (Table 3). There is increasing evidence that dysbiosis of the intestinal microbiota has a role in the pathogenesis of IBD. Up to this date, however, the phylum-level changes observed in IBD patients have not always been consistent. In general, an overall decrease in microbial diversity and stability of the intestinal microbiota has been observed in IBD patients (Hansen et al. 2010). In addition, a decrease in speciﬁc members of the Firmicutes has been reported in IBD patients, which in some cases coincided with an increase in Bacteroidetes and facultative anaerobes such as Enterobacteriaceae (Hansen et al. 2010). Signiﬁcant dif- ferences exist in the microbiota composition of CD patients compared with UC patients (Frank et al. 2007; Sokol et al. 2006). Recently, Joossens and colleagues identiﬁed a set of ﬁve bacterial species that characterised the predominant dysbiosis in CD patients compared with unaffected rela- tives and healthy individuals (Joossens et al. 2011). These ﬁve species are Dialister invisus, an uncharacterised species of Clostridium cluster XIVa, Faecalibacterium prausnitzii, Biﬁdobacterium adolescentis and Ruminococcus 123