220 Table 3 continued Study material Faeces Faeces Faeces Biopsies: inﬂamed and non-inﬂamed tissue (ileum, ascending/transverse/ descending/sigmoid colon, rectum) Population 4 CD patients (in remission) 21 UC patients (in remission) 14 Healthy individuals 68 CD patients (in remission) 84 Unaffected relatives 55 Healthy individuals 16 CD patients (active disease) 16 Healthy individuals 12 CD patients (active disease) 6 UC patients (active disease) 5 Non-IBD controls Analytical methods Clone library sequencing (metagenome) DGGE qPCR qPCR Phylogenetic microarray (16S) qPCR Clone library sequencing (16S) Genes Nutr (2011) 6:209–240 References Qin et al. (2010) Joossens et al. (2011) Mondot et al. (2011) Walker et al. (2011) Most of the studies used the Crohn’s disease activity index (CDAI; for CD) and/or the clinical activity index (CAI; for UC patients) to assess disease activity in the subjects and to deﬁne active disease or remission. 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, RISA ribosomal intergenic spacer analysis, SSCP single strand conformation polymorphism, T-RFLP terminal-restriction fragment length polymorphism, TGGE temperature gradient gel electrophoresis gnavus. Of these species, F. prausnitzii has been associated with prolongation of remission in CD (see also below and Sokol et al. 2008, 2009), while biﬁdobacteria in general have shown to have beneﬁcial effects on health (see above). Most interestingly, the unaffected relatives of CD patients also have a different composition of their pre- dominant microbiota compared with healthy individuals in general. The impact of these observations on IBD diag- nostics and aetiology now has to be addressed. The role of several different microorganisms in the aetiology of IBD has been studied in more detail. Adherent- invasive Escherichia coli (Darfeuille–Michaud 2002; Dar- feuille–Michaud et al. 2004) and Mycobacterium avium subspecies paratuberculosis (Rosenfeld and Bressler 2010) are two prime suspects that have been implicated to be involved in CD pathogenesis. However, a causal relation has not yet been demonstrated. Recently, the presence of two species belonging to the family Enterobacteriaceae, Klebsiella pneumoniae and Proteus mirabilis, was corre- lated with the development of colitis in a mouse model (Garrett et al. 2010). The evidence that speciﬁc micro- organisms can induce intestinal inﬂammation and cause IBD is, however, still inconclusive, despite the considerable amount of studies concerning this subject. In addition to the identiﬁcation of potential pathogenic bacteria, other bacte- rial species have been suggested to protect against IBD. For example, it has been shown that the relative abundance of F. prausnitzii, a commensal bacterium with anti-inﬂam- matory properties, is signiﬁcantly decreased in CD patients compared with healthy individuals (Sokol et al. 2008). 123 High-throughput metagenomic studies can provide more insight in the composition and diversity of the intestinal microbiota of IBD patients. IBD is amongst the ﬁrst diseases that have been the subject of metagenomic investigation (Qin et al. 2010). Based on the relative abundance of 155 microbial species (present in at least one individual at a genome coverage of C1% in this study population), it was possible to separate patients from healthy individuals, and UC from CD patients (Qin et al. 2010). The next step is to compare the IBD subpopula- tions with healthy individuals at microbial gene-level. On average, 25% fewer genes could be detected in the faecal samples of IBD patients compared with individuals not suffering from IBD (Qin et al. 2010). These results sug- gest that the microbiota of IBD patients has a lower functional diversity compared with healthy individuals. The intestinal microbiota in IBD patients produce reduced amounts of SCFA, in particular butyrate, while sulphate reduction (by sulphate-reducing bacteria) is increased (Fava and Danese 2011). In the near future, metagenomic studies like these will provide more insight in the shifts in functionality which characterises the differences between IBD patients and healthy individuals. The observed compositional and functional changes in IBD patients suggest that the intestinal microbiota plays an important role in the aetiology and pathogenesis of IBD. However, up to this date it is still unclear whether dysbiosis is a direct cause for the inﬂammation in IBD, or merely the result of a disturbed environment in the GI tract. In the latter case, a role for the intestinal microbiota in disease