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Table 5 Overview of human studies that demonstrate an association between intestinal disease and compositional dysbiosis of the intestinal microbiota

From: Intestinal microbiota in human health and disease: the impact of probiotics

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)
  1. The intestinal diseases IBD, IBS and obesity are discussed separately in the article
  2. 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