Genes Nutr (2011) 6:209–240 Table 4 continued Study material Faeces (2 time points) Faeces Faeces Faeces Faeces Faeces (2 time points) 31 Monozygotic twin pairs 23 Dizygotic twin pairs 46 Mothers of twin pairs 3 Obese individuals 3 Individuals with a gastric- bypass 3 Normal-weight individuals 15 Obese Indian adolescents 13 Non-obese Indian adolescents 16 Infants of overweight women 26 Infants of normal-weight women 33 Obese individuals 35 Overweight individuals 30 Normal-weight individuals 16 Overweight pregnant women 34 Normal-weight pregnant women Population Analytical methods Key ﬁndings Sanger sequencing (16S) 454 FLX titanium sequencing (metagenome) Clone library sequencing (16S) 454 FLX titanium sequencing (16S) qPCR qPCR FISH/ﬂow cytometry qPCR qPCR GC qPCR Most obesity-associated genes are from: Actinobacteria Firmicutes Most lean-enriched genes are from Bacteroidetes Obese individuals: : H2-producing Prevotellaceae : H2-utilizing methanogenic Archaea Obese children: $ Bacteroides-Prevotella $ Biﬁdobacterium $ L. acidophilus $ E. rectale : F. prausnitzii Infants of overweight mothers: : Bacteroides : Staphylococcus Obese individuals compared with lean: : Bacteriodetes ; Firmicutes Overweight pregnant women: ; Biﬁdobacterium ; Bacteroides : Staphylococcus : Enterobacteriaceae : E. coli 223 References Turnbaugh et al. (2009) Zhang et al. (2009) Balamurugan et al. (2010) Collado et al. (2010)# Schwiertz et al. (2010) Santacruz et al. (2010) 123 All studies have used the body mass index (BMI) to deﬁne normal weight, overweight and obesity. Studies that have used subjects from the same cohort are indicated by *, # and FISH ﬂuorescence in situ hybridisation, GC gas chromatography, qPCR quantitative polymerase chain reaction and Delzenne 2009; Ley 2010; Vrieze et al. 2010). In a recent study, a high-throughput sequencing approach was used to demonstrate that type 2 diabetes, a metabolic dis- ease primarily caused by obesity-linked insulin resistance, is associated with changes in the composition of the intestinal microbiota (Larsen et al. 2010). The relative abundance of Firmicutes was signiﬁcantly lower in dia- betic patients compared with non-diabetic persons. On the other hand, the Bacteroidetes and Proteobacteria were present in higher abundance. In addition, the Bacteroidetes/ Firmicutes and Bacteroides-Prevotella/C.coccoides-E.rec- tale ratios were positively and signiﬁcantly correlated with plasma glucose levels. Microbial diversity and other human diseases In addition to IBD, IBS and obesity, the intestinal micro- biota has also been suggested to be involved in several other (chronic) diseases and disorders. Associations have been described between intestinal microbial dysbiosis and intestinal diseases such as coeliac disease, colorectal cancer, pouchitis and necrotizing enterocolitis (NEC) (Table 5). The most recent data show that the intestinal microbiota of coeliac disease patients displays a greater diversity than healthy controls with higher numbers of Bacteroides-Prevotella (De Palma et al. 2010; Schippa et al. 2010). Biﬁdobacterium, Clostridium histolyticum, C.