Table 5.

Overview of human studies that demonstrate an association between intestinal disease and compositional dysbiosis of the intestinal microbiota

Study material	Population	Analytical methods	Reference
Coeliac disease
Faeces	26 Coeliac patients (no diet, active disease) 23 Children without gluten intolerance	Conventional culturing FISH	Collado et al. (2007)
Duodenal biopsies	20 Coeliac patients (no diet, active disease) 10 Coeliac patients (gluten-free diet, symptom-free) 8 Children without gluten intolerance	FISH/flow cytometry	Nadal et al. (2007)
Faeces	10 Coeliac patients (no diet, active disease) 10 Children without gluten intolerance	DGGE	Sanz et al. (2007)
Duodenal biopsies faeces	30 Coeliac patients (no diet) 18 Coeliac patients (gluten-free diet) 30 Children without gluten intolerance	qPCR	Collado et al. (2008a)
Faeces	24 Coeliac patients (no diet, active disease) 18 Coeliac patients (gluten-free diet, symptom-free) 20 Children without gluten intolerance	FISH/flow cytometry	De Palma et al. (2010)
Duodenal biopsies	20 Coeliac patients (active disease/symptom-free) 10 Children without gluten intolerance	TGGE	Schippa et al. (2010)
Colorectal cancer
Faeces	18 Patients with polyps 32 Individuals with high -risk for colon cancer 38 Individuals with low-risk for colon cancer	Conventional culturing	Moore and Moore (1995)
Faeces	13 Patients at high risk for sigmoid colon cancer 14 Healthy individuals	Conventional culturing	Kanazawa et al. (1996)
Faeces (3 time points)	20 Colon cancer patients 20 Polypectomized patients 20 Healthy individuals	DGGE	Scanlan et al. (2008)
Colorectal biopsies	21 Individuals with adenomas 23 Individuals without adenomas	T-RFLP Clone library sequencing (16S) FISH	Shen et al. (2010)
Pouchitis
Pouch biopsies Ileostomy effluent Faeces	12 Patients with pouchitis 14 Patients with indeterminable pouchitis 23 Patients without pouchitis 20 Ileostomy patients 9 Healthy individuals	Conventional culturing	Onderdonk et al. (1992)
Pouch effluent	5 Patients with pouchitis 9 Patients without pouchitis	Conventional culturing	Ruseler-van Embden et al. (1994)
Pouch effluent	UC patients:  8 Patients with healthy pouches  9 Patients, no active pouchitis for at least 1 year  9 Patients, no active pouchitis for at least 6 weeks  11 Patients with pouchitis, on antibiotic treatment  8 Patients with pouchitis FAP patients:  5 Patients with healthy pouches	Conventional culturing	Ohge et al. (2005)
Pouch effluent	9 Patients with pouchitis (UC) 13 Patients with healthy pouches (UC)	Conventional culturing	Iwaya et al. (2006)
Ileum biopsies Pouch biopsies Pouch effluent	5 Patients with pouchitis (UC) 15 Patients with healthy pouches (UC) 13 Healthy individuals	LH-PCR Clone library sequencing (16S)	Komanduri et al. (2007)
Pouch effluent	5 Patients with pouchitis (UC) 15 Patients with healthy pouches (UC)	T-RFLP Clone library sequencing (16S)	Lim et al. (2009)
Pouch contents Pouch biopsies	9 Patients with pouchitis (UC) 3 Patients with healthy pouches (UC) 7 Patients with healthy pouches (FAP)	T-RFLP Clone library sequencing (16S)	Zella et al. (2011)
Necrotizing enterocolitis
Faeces	10 Preterm infants with NEC 10 Preterm infants without NEC	T-RFLP Clone library sequencing (16S)	Wang et al. (2009)
Faeces (several time points)	6 Preterm infants with NEC or suspected sepsis 6 Preterm control infants	DGGE 454 FLX titanium sequencing (16S)	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 polymorphism, TGGE temperature gradient gel electrophoresis, UC ulcerative colitis