216 two age groups (Biagi et al. 2010). The microbiota of centenarians was characterised by low species-level diversity, speciﬁc changes in Firmicutes subpopulations, enrichment in Proteobacteria and a decrease in biﬁdo- bacteria. In addition, high-throughput next generation sequencing has been used by Claesson and colleagues to study the composition, variability and temporal stability of the intestinal microbiota of the elderly (Claesson et al. 2010). They observed that the faecal microbiota of elderly individuals was relatively stable over a 3 month period in the majority of the subjects. However, compared with younger control subjects, the microbiota of the elderly was characterised by a high inter-individual variation in microbiota composition, also at phylum level. The relative abundance of the Firmicutes varied between 8% and 80%, whereas the Bacteroidetes levels varied between 14% and 92%. Furthermore, it was found that in the majority of the elderly subjects the microbiota was characterised by a higher Bacteroidetes/Firmicutes ratio compared with that observed in younger adults. In addition, distinct differences were seen in Proteobacteria, Actinobacteria and Clos- tridium populations between young and older adults. With respect to human health, associations have been found between microbiota composition and frailty in elderly individuals (Van Tongeren et al. 2005). In frail elderly persons, a signiﬁcant reduction in the number of lacto- bacilli, Faecalibacterium prausnitzii and Bacteroides- Prevotella groups was seen. In contrast, the number of Enterobacteriaceae was signiﬁcantly higher. The number of studies that have focused on the age-related differences in intestinal microbiota composition is still limited. In general, they suggest that maintenance of (microbial) homeostasis in the GI tract is essential for healthy ageing. Microbial diversity and IBS IBS is a functional bowel disorder which is characterised by recurrent abdominal pain or discomfort, irregular bowel movements and disordered stool patterns such as consti- pation or diarrhoea (Longstreth et al. 2006). The occur- rence of these symptoms, however, can vary from person to person. The aetiology of IBS is probably complex and still not well understood. Several factors are thought to be involved in IBS and may include altered GI motility, visceral hypersensitivity, low-grade inﬂammation, and psychosocial (anxiety and depression), genetic and dietary factors (Chang and Talley 2011; Karantanos et al. 2010). Several studies, using both culture-dependent and independent methods, have demonstrated an association between IBS and dysbiosis of the intestinal microbiota (Table 2). In general, faecal material has been used to study dysbiosis in IBS patients. However, more recently also duodenal (Kerckhoffs et al. 2009, 2010) and colonic 123 Genes Nutr (2011) 6:209–240 (Carroll et al. 2010; Codling et al. 2010) biopsies have been used to study the mucosa-associated microbiota. Most studies aimed to show changes in the predominant micro- bial communities, however, in some cases the focus was more on speciﬁc microbial groups. Quantitative differences in microbiota composition, even for speciﬁc microbial groups, have been observed in IBD patients compared with healthy individuals. However, the results of the various studies are inconsistent and no consensus has been reached on the association between speciﬁc microbial groups and IBS, notably as the power of the studies was low and the depth of the analysis was limited (Salonen et al. 2010a). At the functional level, some studies have demonstrated altered colonic fermentation patterns and increased gas production in IBS patients (Koide et al. 2000; Mortensen et al. 1987; Tana et al. 2010; Treem et al. 1996). However, these results have not yet been conﬁrmed in other studies at the molecular level. In most of the studies, IBS patients have been classiﬁed into different subtypes based on Rome II criteria for IBS: diarrhoea-predominant IBS (IBS-D), constipation- predominant IBS (IBS-C) or a mixed type of IBS with alternating stool patterns (IBS-A). Distinct changes in microbiota composition have been observed in the different IBS subtypes compared with healthy individuals (Malinen et al. 2005; Maukonen et al. 2006; Lyra et al. 2009). It appears that the intestinal microbiota of IBS-D patients deviates the most from that of healthy individuals (Carroll et al. 2010; Krogius–Kurikka et al. 2009). These data demonstrate the relevance of clinical subtyping of IBS patients when analysing the intestinal microbiota. So far, however, the results from the studies which have applied IBS subtyping have also not shown uniform changes in microbial composition (Salonen et al. 2010a). Microbial diversity and IBD IBD is a collective name for chronic inﬂammatory disorders of the GI tract, of which Crohn’s disease (CD) and ulcerative colitis (UC) are the most prevalent forms. These are both chronic and relapsing diseases that affect the intestinal mucosa. For both CD and UC, the exact aetiology is still not clear, however, it is has been suggested that an aberrant immune response directed against intestinal microbial antigens is involved (Hansen et al. 2010; Sartor 2008; Sokol and Seksik 2010). CD affects the whole GI tract and is characterised by discontinuous inﬂammation of the epithe- lial lining and deep ulcers. UC on the other hand is restricted to the colon and the rectum and is characterised by a con- tinuous mucosal inﬂammation and superﬁcial ulcers. During the last decade, numerous culture-independent studies have compared the intestinal microbiota composi- tion of IBD patients with that of healthy individuals