Genes Nutr (2011) 6:209–240 part of this diversity can be attributed to genetic differences amongst hosts. A positive relation between similarity in dominant faecal microbial communities and genetic related- ness of the hosts has been observed (Stewart et al. 2005; Turnbaugh et al. 2009; Zoetendal et al. 2001). It is esti- mated that more than 1,000 species-level phylotypes can be found in the GI tract of the total human population (Qin et al. 2010; Rajilic´-Stojanovic´ et al. 2007). However, the phylogenetic diversity in one individual is much lower, since the intestinal microbiota of each individual only consists of approximately 160 different bacterial species (Qin et al. 2010). This estimation is based on metagenomic analysis using the number of non-redundant genes con- tained by an average-sized genome. Despite the high species richness and inter-individual variability of the intestinal microbiota, a limited number of bacterial phylo- types is more prevalent amongst individuals and might therefore represent a shared phylogenetic core (Qin et al. 2010; Tap et al. 2009). However, the estimation of the size of the phylogenetic core is dependent on the minimal rel- ative abundance of a given phylotype that can be detected by the molecular approaches deployed. Recent analysis of metagenomic data indicated that there is a high variability in relative abundance (evenness) of core phylotypes amongst individuals (12- to 2,200-fold difference) (Qin et al. 2010). Altogether, these results demonstrate that an accurate estimation of the size of the phylogenetic core is still difﬁcult to make as this is highly dependent on the depth of the analysis. The vast majority of all microbial cells in the human GI tract are bacteria. At the phylum-level, both culture- dependent and independent studies have demonstrated that the majority of the intestinal bacteria belong to two phyla, the Bacteroidetes and the Firmicutes (Mariat et al. 2009). The phylum Bacteroidetes consists of three classes, of which the class Bacteroidetes, containing the well-known genera Bacteroides and Prevotella, is probably the most well studied. The Firmicutes is currently the largest bacte- rial phylum, which contains more than 200 genera. The majority of the Firmicutes detected in the GI tract fall pri- marily into two main groups, the Clostridium coccoides group (also known as Clostridium cluster XIVa) and the Clostridium leptum group (also referred to as Clostridium cluster IV) (Collins et al. 1994; Mariat et al. 2009). Both groups contain members of the genera Clostridium, Eubacterium and Ruminococcus that are taxonomically polyphyletic. In addition to the two phyla Bacteroidetes and Firmicutes, also members of other phyla, such as Proteo- bacteria, Actinobacteria, Fusobacteria, Spirochaetes, Verrucomicrobia and Lentisphaerae, have been detected (Rajilic´-Stojanovic´ et al. 2007; Zoetendal et al. 2008). Although bacteria dominate the GI tract ecosystem, species from the archaeal domain can also be found in the 211 GI tract, with the methanogens, Methanobrevibacter smi- thii and Methanosphaera stadtmanae being by far the most dominant archaeal groups (Gill et al. 2006; Mihajlovski et al. 2008). While it was previously assumed that these methanogens were only present in a minor fraction of healthy subjects, application of new DNA isolation meth- ods has led to the observation that they are in fact highly prevalent (Dridi et al. 2009; Salonen et al. 2010b). In addition to bacteria and archaea, eukaryotic micro- organisms can also be members of the intestinal micro- biota. Culture-independent analysis of the fungal diversity in the GI tract has demonstrated that the majority of the phylotypes belonged to the two fungal phyla Ascomycota (which includes the genera Candida and Saccharomyces) and Basidiomycota (Ott et al. 2008; Scanlan and Marchesi 2008). Microbial diversity along the GI tract Host physiology and intestinal microbiota are intimately connected. This is evident from the fact that each distinct anatomical region along the GI tract is characterised by its own physicochemical conditions, and that these changing conditions exert a selective pressure on the microbiota. The physicochemical conditions that inﬂuence the composition of the intestinal microbiota include intestinal motility, pH, redox potential, nutrient supplies, host secretions (e.g. hydrochloric acid, digestive enzymes, bile and mucus), and the presence of an intact ileocaecal valve (Booijink et al. 2007). Thus, the GI tract harbours many distinct niches, each containing a different microbial ecosystem that varies according to the location within the GI tract. This is already demonstrated by the fact that the microbial density increases along the GI tract. Per gram of intestinal content, the microbial density increases from 101–104 microbial cells in the stomach and duodenum, 104–108 cells in the jejunum and ileum, to 1010–1012 cells in the colon and faeces (Booijink et al. 2007; Dethlefsen et al. 2006). Despite the fact that it is well known that the intestinal microbiota is not homogeneously distributed within the GI tract, it is still largely unknown how the diversity varies in the different niches along the GI tract (‘who is present where’). By far, the most detailed knowledge is available with respect to the microbial composition of faeces. This is mainly because faecal material can be collected non- invasively and contains a large biomass of microbial cells. However, as it is increasingly acknowledged that the composition of microbiota differs signiﬁcantly in the dif- ferent niches, more efforts are undertaken to determine the spatio-temporal dynamics of the microbial diversity along the whole GI tract (Zoetendal et al. 2002). The large intestine has a rather uniform composition of luminal 123