Genes Nutr (2011) 6:209–240 Table 5 continued Study material Pouch efﬂuent Ileum biopsies Pouch biopsies Pouch efﬂuent Pouch efﬂuent Pouch contents Pouch biopsies Necrotizing enterocolitis Faeces Faeces (several time points) Population 9 Patients with pouchitis (UC) 13 Patients with healthy pouches (UC) 5 Patients with pouchitis (UC) 15 Patients with healthy pouches (UC) 13 Healthy individuals 5 Patients with pouchitis (UC) 15 Patients with healthy pouches (UC) 9 Patients with pouchitis (UC) 3 Patients with healthy pouches (UC) 7 Patients with healthy pouches (FAP) 10 Preterm infants with NEC 10 Preterm infants without NEC 6 Preterm infants with NEC or suspected sepsis 6 Preterm control infants 225 Analytical methods Reference Conventional culturing Iwaya et al. (2006) LH-PCR Clone library sequencing (16S) T-RFLP Clone library sequencing (16S) T-RFLP Clone library sequencing (16S) T-RFLP Clone library sequencing (16S) DGGE 454 FLX titanium sequencing (16S) Komanduri et al. (2007) Lim et al. (2009) Zella et al. (2011) Wang et al. (2009) Mshvildadze et al. (2010) The intestinal diseases IBD, IBS and obesity are discussed separately in the article DGGE denaturing gradient gel electrophoresis, FAP familial anastomosis polyposis, FISH ﬂuorescence in situ hybridisation, LH-PCR length heterogeneity polymerase chain reaction, qPCR quantitative polymerase chain reaction, T-RFLP terminal-restriction fragment length poly- morphism, TGGE temperature gradient gel electrophoresis, UC ulcerative colitis lituseburense and F. prausnitzii were less abundant in coeliac disease patients (De Palma et al. 2010). Also in the case of colorectal cancer, the bacterial diversity and rich- ness was observed to be higher in patients compared with healthy controls (Shen et al. 2010). In addition, the intes- tinal microbiota composition of colorectal cancer patients differs from that of healthy controls, however, no consis- tent pattern has yet been observed. The mucosal and faecal microbiota of UC pouchitis patients contained more Clostridium and Eubacterium and fewer Lactobacillus and Streptococcus genera compared with the microbiota of healthy pouches from familial adenomatous polyposis (FAP) patients (Lim et al. 2009; Zella et al. 2011). Luminal samples of UC pouchitis patients contained more Firmicutes and Verrucomicrobia and fewer Bacteroidetes and Proteobacteria compared with FAP patients. The overall microbiota proﬁles of premature infants with necrotizing enterocolitis (NEC) were not distin- guishable from that of control subjects, but 16S rRNA gene sequence analysis detected Citrobacter-like sequences and an increased frequency of Enterococcus-like sequences (Mshvildadze et al. 2010). Intestinal microbial dysbiosis has also been observed in extra-intestinal diseases such as atopic and allergic dis- eases, autism, type 2 diabetes and rheumatoid arthritis (Table 6). In children who develop an allergic disease later in life, a reduced diversity of faecal microbiota was already observed at 1 week of age (Wang et al. 2009; Niers et al., personal communication). During the ﬁrst 2 months of life, they were less often colonised with lactobacilli group I (L. rhamnosus, L. casei, L. paracasei), B. adolescentis and Clostridium difﬁcile (Kallioma¨ki et al. 2001; Sjo¨gren et al. 2009). The number of Clostridium species found in the stools of children with autism was greater than in the stools of control children, speciﬁcally of the C. histolyticum group (Clostridium clusters I and II) (Finegold et al. 2002; Par- racho et al. 2005). Bacteroidetes was found at high levels in the severely autistic children while populations of the Biﬁdobacterium genus were reduced (Finegold et al. 2010). Firmicutes and Clostridia are reduced in type 2 diabetes (Larsen et al. 2010). Furthermore, the Bacteroidetes/Fir- micutes ratio as well as Bacteroides-Prevotella/C. cocco- ides-E. rectale ratio were observed to be correlated with plasma glucose concentration. In a Chinese population of diabetes patients, reduced populations of biﬁdobacteria were found (Wu et al. 2010). In comparison to patients with ﬁbromyalgia, patients with rheumatoid arthritis had signiﬁcantly less biﬁdobac- teria and bacteria of the Bacteroides-Prevotella group, Bacteroides fragilis subgroup, and E. rectale-C. coccoides group (Vaahtovuo et al. 2008). Almost all of the diseases and disorders mentioned above are largely undeﬁned and have a heterogeneous aetiology, which makes it difﬁcult to relate changes in 123