Genes Nutr (2011) 6:209–240 both signiﬁcantly from distal colonic mucosa-associated samples (Wang et al. 2010). In addition, the study demon- strated that the region-speciﬁc mucosa-associated microbiota determines the region-speciﬁc expression of host genes, in this case of genes encoding Toll-like receptors (TLRs). Due to the application of culture-independent molecular approaches, our knowledge of the intestinal microbiota has been advanced signiﬁcantly (Zoetendal et al. 2006). Yet, a complete description of the microbial diversity along the human GI tract cannot be given at this moment. Future research should include more samples from the various distinct niches along the GI tract, which nowadays can be collected using minimally invasive methods and which can be deeply analysed using high-throughput technologies. Functional diversity of the intestinal microbiota Recently, the collective genome of the human intestinal microbiota (the human intestinal microbiome) was estimated to contain 3.3 million microbial genes, which is *150 times more genes than the human genome (Qin et al. 2010). The presence of this wide array of genes in addition to our own genome, suggests that a profound inﬂuence of intestinal microorganisms on the human body can be expected. This means that meaningful information related to human health does not only originate from insights in the compositional diversity (‘who is present’, ‘with how many are they present’ and ‘who is present where’), but can also be derived from knowledge on the function of the microbiota (‘what are they doing’). The extent to which the intestinal microbiota is able to expand the metabolic, nutritional, physiological and immunological functions the host is able to perform, is still largely unknown. To address this question, metagenomic studies can provide information on the diversity of the genes encoded by the intestinal microbiota. Recently, it was cal- culated that almost 40% of the microbial genes present in each human individual were shared with at least half of the human individuals in the studied cohort. These data provide evidence for the existence of a functional core (core micro- biome) (Qin et al. 2010). Since functional redundancy within members of the intestinal microbiota exists, there is the possibility that the phylogenetic core does not fully correspond to the functional core (Zoetendal et al. 2008). The functional core may contain shared metabolic functions (e.g. degradation of sugar monomers, production of vitamins or butyrate formation) as well as sequential pathways which would, respectively, restrict or expand functional diversity irrespective of phylogenetic diversity. A main focus of current research is to understand the functional contribution of the human intestinal microbiota to the host. Function-driven metagenomics is a ﬁrst step in assessing the functional capacity of the intestinal micro- biota. A prediction of the functional capacity can originate 213 from the metagenome by comparing the assembled sequences to reference databases, such as the COG (clusters of orthologous groups) and KEGG (Kyoto encyclopedia of genes and genomes) databases. Moreover, function-driven metagenomics can be applied to assign a function to predicted gene products and can even contribute to gene discovery (Tasse et al. 2010; Cowan et al. 2005). The ﬁrst metagenomic studies have demonstrated that, compared with the human genome, the human intestinal microbiome is highly enriched for COG and KEGG categories involved in metabolism (Gill et al. 2006; Kurokawa et al. 2007; Turnbaugh et al. 2009). Pathways involved in metabolism of energy, amino acids, nucleotides, carbohydrates, cofac- tors and vitamins, terpenoids and polyketides, and the bio- synthesis of secondary metabolites are highly represented in the human microbiome. These pathways not only allow the microbes to generate energy, to grow and proliferate, but also to inﬂuence the host. Some of the metabolites are being taken away from the host while other ones are provided (e.g. SCFA, vitamins, gases). Overall, the (metabolic) interaction between microbes and host is beneﬁcial for both parties. Future studies should provide data to further establish and detail the functional contribution of the intestinal micro- biota to the metabolic capacity of the host. Metagenomic studies provide only insight in the genetic potential of the intestinal microbiota and do not demon- strate its true functional contribution to the maintenance of health and well-being (Zoetendal et al. 2008). In order to obtain insights in the in situ expression of genes encoded by the intestinal microbiome, other functional microbiomic approaches, such as metatranscriptomics, metaproteomics and metabolomics are required. A recent example of a metatranscriptomic approach to study the intestinal micro- biota is provided by the study performed by Booijink et al. (2010). These authors were able to demonstrate that the gene expression of the human faecal microbiota is subject-speciﬁc and enriched for genes involved in (car- bohydrate) metabolism. Gosalbes and colleagues also applied a metatranscriptomic approach to study the func- tionality of the faecal microbiota of healthy volunteers (Gosalbes et al. 2011). Remarkably, more rRNA genes were observed than protein-encoding genes. Analysis of the latter showed a uniform functional pattern in carbo- hydrate metabolism, energy production and synthesis of cellular components as well as regulatory elements (small RNAs). More speciﬁc information has been derived from the metatranscriptomic analysis of biﬁdobacteria in early life that revealed marked differences between breast-fed and formula-fed infants. Moreover, the speciﬁc expression of genes involved in the degradation of human-derived sugars and vitamins such as folic acid biosynthesis testify for the health impacting function of intestinal biﬁdobac- teria (Klaassens et al. 2009). Furthermore, metaproteomics 123