214 approaches have been applied to investigate faecal samples obtained from human infants (Klaassens et al. 2007) and adults (Rooijers et al. 2011; Verberkmoes et al. 2009). In human adults, it was demonstrated that the faecal meta- proteome is enriched in proteins belonging to the COG categories involved in translation, energy production and carbohydrate metabolism (Verberkmoes et al. 2009). Compared with metatranscriptomics and metaproteomics approaches, metabolomic approaches have up to this date been applied more frequently, using NMR spectroscopy and mass spectroscopy in conjunction with computational multivariate analysis (Nicholson and Lindon 2008). A recent study by Martin and colleagues demonstrates that metabolic proﬁling can be used for studying nutrient- microbiota relations by examining the effects of dietary intervention on the presence of faecal metabolites (Martin et al. 2010). A variety of systemic diseases such as hypertension (Holmes et al. 2008) and diabetes (Dumas et al. 2007) appear to be directly inﬂuenced by microbial metabolism in model animals and human (Kinross et al. 2011). The metabolic pathways that are involved in drug metabolism are also inﬂuenced by the intestinal microbiota in an in vitro system (Aura et al. 2011). Altogether, functional microbiomic approaches can be applied to examine microbial gene expression and to estab- lish the effects of microbial gene products on the host. However, up to this date it is difﬁcult to connect functionality to the presence of individual microbial species in the human GI tract. In order to link speciﬁc sets of genes to the presence of distinct microbial species, complete microbial genome sequences will be needed. Several independent research consortia have taken up the effort to sequence the genomes of hundreds of bacterial strains, which together will form a catalogue of reference genomes from the human microbiota. Recently, the initial sequencing of 178 reference genomes was reported and the ﬁrst results of comparative genomic analysis of these sequences provided important insight into the inter-strain diversity of bacterial genomes (Nelson et al. 2010). Large-scale functional microbiomic analyses are needed to fully understand the impact of the human microbiome on the host. This means that a larger number of samples, deeper sequencing, longer sequence reads and more extensive comparative analyses are needed. Integration of all these microbiomic approaches will help to deﬁne the func- tional contribution of each individual microbial phylotype in the human GI tract to the health status of the host. Changes in composition and diversity of the intestinal microbiota are related to disease The type and number of microbial species that persist and colonise the GI tract is not determined by chance, but by a 123 Genes Nutr (2011) 6:209–240 combination of factors including but not limited to the inﬂammatory state of the host, diet, host genetics, and environmental factors (Buddington and Sangild 2011; Cerf–Bensussan and Gaboriau–Routhiau 2010; Hansen et al. 2010; Musso et al. 2010). This means that the host itself inﬂuences the composition of the intestinal micro- biota. However, the relative impact of these factors on the intestinal microbiota is still largely unknown. The intestinal microbiota and the host have co- evolved (Ley et al. 2008). Human evolution has taken place amidst a world of microorganisms. Symbiotic microorganisms have occupied the niches offered by the gastrointestinal tract and probably adapted to the local circumstances. This in turn may have inﬂuenced human evolution in terms of metabolic and nutritional require- ments. Ultimately, man depends on its intestinal micro- biota for a number of vital functions and thus these intestinal microorganisms may contribute to health. It is, however, difﬁcult to describe the precise impact of the intestinal microbiota on human health and the involve- ment in human disease. Perturbation of the microbiota composition, also known as dysbiosis, has been recognised in various diseases, of which many are associated with the GI tract. However, before dysbiosis can be established, the composition of a healthy ‘normal’ microbiota has to be deﬁned. Yet, the deﬁnition of a healthy microbiota is not easy to give. From an operational point of view it could be stated that a healthy intestinal microbiota is the microbiota composi- tion as it can be found in healthy individuals. For prac- tical reasons, the phylogenetic characterisation of the microbiota of diseased individuals in comparison with apparently healthy individuals is, at this moment, the main approach to study changes in composition of the intestinal microbiota in relation to disease. However, since there are substantial inter-individual and intra- individual variations in the composition of the intestinal microbiota, it is difﬁcult to establish the precise relations between human health and the presence and relative abundance of speciﬁc microbial communities. In the future, speciﬁc changes in compositional diversity, or even functional diversity, may be applied as biomarkers for health or speciﬁc diseases. It must be noted, however, that it is questionable whether changes in phylogenetic composition are really cause or consequence of a given disease. A role for the intestinal microbiota in the pathogenesis of several diseases and disorders has been suggested. Intensively studied examples for which dysbiosis of the intestinal microbiota has been described, include inﬂam- matory bowel disease (IBD), irritable bowel syndrome (IBS) and obesity, which will be discussed in-depth in this part of the review.