210 Cerf–Bensussan and Gaboriau–Routhiau 2010; O’Hara and Shanahan 2006; Sekirov et al. 2010; Zoetendal et al. 2008). In recent years, a sharp increase is seen in the number of publications addressing the intestinal microbiota. They have provided various lines of evidence supporting a close link between the intestinal microbiota and human health. This review aims to summarise the current knowledge on the composition and diversity of the intestinal microbiota. In addition, it is discussed how new molecular approaches have provided novel insights towards the phylogenetic and functional characterisation of the intestinal microbiota. Furthermore, recent insights on the link between the intestinal microbiota and human health are provided. Finally, an overview is presented of ways to modulate the intestinal microbiota with speciﬁc attention for the use of probiotics, deﬁned as live microorganisms which, when administered in adequate amounts, confer a health beneﬁt on the host (FAO/WHO 2002). Microbial diversity in the GI tract The GI tract is a complex and dynamic ecosystem con- taining a diverse collection of microorganisms. These microorganisms are either resident members of the intes- tinal microbiota or transient passengers introduced from the environment, for example by the regularly inﬂux of microorganisms by the intake of food. Compositional diversity of the intestinal microbiota The intestinal microbiota can be described in richness (‘who is present’) and evenness (‘with how many are they present’) that together form the ecological terms of diver- sity. If applied at the species-level, richness describes the number of species present in a speciﬁc ecosystem, not taking into account their relative abundance. This contrasts with evenness, which represents the relative abundance of Genes Nutr (2011) 6:209–240 each species in a speciﬁc ecosystem. These deﬁnitions are used to describe the microbial diversity in the GI tract. Up till recently, conventional culture-based methods were used to assess the intestinal microbial diversity. Over 400 bacterial species have been successfully isolated, cul- tured and characterised from the human GI tract (Rajilic´- Stojanovic´ et al. 2007). However, these culture-based methods have proven to be inadequate in determining the true microbial diversity of the intestinal microbiota since a large fraction of the microbiota remains uncultivated. For a more accurate analysis of the compositional diversity of the intestinal microbiota culture-independent approaches have been developed and it has been revealed that the human intestinal microbiota is an even more complex ecosystem than previously expected. Most of these techniques target the highly conserved 16S ribosomal RNA (rRNA) gene sequences of bacterial and archaeal microorganisms. Molecular techniques that are used to study the diversity of the intestinal microbiota include quantitative polymerase chain reaction (qPCR), temperature or denaturing gradient gel electrophoresis (TGGE or DGGE), terminal-restriction fragment length polymorphism (T-RFLP) and ﬂuorescent in situ hybridisation (FISH). The latest developments in high-throughput technologies, such as next generation sequencing and phylogenetic micro-arrays, now allow more in-depth analysis of the complete phylogenetic diversity of the intestinal microbiota (Van den Bogert et al. 2011; Zoetendal et al. 2008). Moving beyond the analysis of the variation in the sequence of a single marker gene, it is currently also possible to characterise the complete genetic material obtained from environmental samples such as the GI tract. With the aid of large-scale sequencing approaches these so called metagenomes can be studied and so far several metagenomic inventories of the intestinal microbiota have been reported (Table 1). Since the ﬁrst application of culture-independent meth- ods to determine diversity, it has been shown that the composition of the intestinal microbiota varies substan- tially amongst individuals (Zoetendal et al. 1998). At least Table 1 Overview of metagenomic studies of the human intestinal microbiota Nationality of individuals American Japanese American European (Danish or Spanish) European French 123 Number of individuals 2 13 18 124 20 49 Sequencing technology Sanger Sanger 454 FLX Titanium Solexa (Illumina) Sanger SoliD Total length of sequences obtained (Gb) 0.2 0.727 2.14 576.7 2.6 200 References Gill et al. (2006) Kurokawa et al. (2007) Turnbaugh et al. (2009) MetaHIT Qin et al. (2010) Genescope INRA