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Table 3 Overview of human studies that demonstrate an association between IBD and compositional dysbiosis of the intestinal microbiota determined with culture-independent methods

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

Study material Population Analytical methods References
Biopsies (terminal ileum, colon) 12 CD patients (active disease)
12 UC patients (active disease)
14 Non-IBD controls
FISH Kleessen et al. (2002)
Biopsies: inflamed and non-inflamed tissue (ileum, ascending/sigmoid colon) 28 Self-limiting colitis patients
104 Indeterminate colitis patients
119 UC patients
54 CD patients
40 Non-IBD controls
Conventional culturing
qPCR
FISH
Swidsinski et al. (2002)
Faeces 8 CD patients (active disease)
9 CD patients (in remission)
16 Healthy individuals
Dot-blot hybridisation
TGGE
Seksik et al. (2003)
Faeces 4 CD patients
4 Healthy controls
Clone library sequencing (16S) Mangin et al. (2004)
Colonic biopsies: inflamed tissue 26 CD patients (active disease)
31 UC patients (active disease)
15 Inflammatory controls
31 Non-inflammatory controls
SSCP
Clone library sequencing (16S)
qPCR
Ott et al. (2004)
Rectal biopsies: inflamed and non-inflamed tissue 4 CD patients (active disease)
2 CD patients (in remission)
14 UC patients (active disease)
19 UC patients (in remission)
14 Non-IBD controls
FISH Mylonaki et al. (2005)
Biopsies: inflamed and non-inflamed tissue (ileum, ascending/sigmoid colon) 20 CD patients
20 UC patients
20 Self-limiting colitis patients
20 IBS patients
20 Non-IBD controls
FISH Swidsinski et al. (2005)
Biopsies: inflamed and non-inflamed tissue (ileum, ascending/transverse/descending colon, rectum) 20 CD patients (active disease)
15 UC patients (active disease)
14 Non-IBD controls
Clone library sequencing (16S)
DGGE
qPCR
Bibiloni et al. (2006)
Biopsies: inflamed and non-inflamed tissue (ileum, transverse/sigmoid colon, rectum) 6 CD patients
5 UC patients
5 Non-IBD controls
Clone library sequencing (16S) Gophna et al. (2006)
Faeces 6 CD patients (in remission)
6 Healthy individuals
Clone library screening (metagenome: 16S)
FISH/flow cytometry
Manichanh et al. (2006)*
Biopsies: inflamed and non-inflamed tissue (ileum, ascending/transverse/descending/sigmoid colon, rectum) 19 CD patients
2 UC patients
1 Ischemic colitis patient
15 Non-IBD controls
DGGE
16S rRNA gene sequence analysis
Martinez–Medina et al. (2006)
Faeces (several time points) 16 CD patients
18 Healthy individuals
DGGE Scanlan et al. (2006)
Faeces 13 CD patients (active disease)
13 UC patients (active disease)
5 Infectious colitis patients
13 Healthy individuals
FISH/flow cytometry Sokol et al. (2006)#
Faeces 29 UC patients (active disease)
12 UC patients (in remission)
46 Healthy individuals
T-RFLP Andoh et al. (2007)
Ileal biopsies 13 CD patients (ileum)
8 CD patients (colon)
7 Non-IBD controls
Clone library sequencing (16S)
qPCR
FISH
Baumgart et al. (2007)
Biopsies (small intestine and colon) 68 CD patients
61 UC patients
61 Non-IBD controls
Clone library sequencing (16S)
qPCR
Frank et al. (2007)
Biopsies (caecum, colon, rectum) 13 CD patients
19 UC patients
15 Healthy individuals
RISA
Conventional culturing
Kotlowski et al. (2007)
Faeces 17 CD patients (active disease)
17 CD patients (in remission)
20 Healthy controls
T-RFLP Andoh et al. (2008)
Faeces 10 Twin pairs with CD
8 Healthy twin pairs
G+C profiling
Clone library sequencing (16S)
T-RFLP
Dicksved et al. (2008)
Faeces (several time points) 16 UC patients (in remission)
8 Healthy controls
DGGE Martinez et al. (2008)
Colonic biopsies
Faeces
15 CD patients (active disease)
8 CD patients (in remission)
44 UC patients (active disease)
29 UC patients (in remission)
Conventional culturing
qPCR
FISH
HPLC
Takaishi et al. (2008)
Rectal biopsies: inflamed and non-inflamed tissue 9 UC patients (active disease)
11 Non-IBD controls
T-RFLP Nishikawa et al. (2009)
Faeces 22 CD patients (active disease)
10 CD patients (in remission)
12 UC patients (active disease)
4 UC patients (in remission)
8 Infectious colitis patients
27 Healthy individuals
qPCR Sokol et al. (2009)#
Biopsies (terminal ileum, ascending/transverse/descending colon, rectum) 10 Twin pairs with CD
8 Healthy twin pairs
T-RFLP
Clone library sequencing (16S)
qPCR
Willing et al. (2009)
Faeces 6 CD patients (in remission)
6 Healthy individuals
qPCR
Phylogenetic microarray (16S)
Kang et al. (2010)*
Faeces 4 CD patients (in remission)
21 UC patients (in remission)
14 Healthy individuals
Clone library sequencing (metagenome) Qin et al. (2010)
Faeces 68 CD patients (in remission)
84 Unaffected relatives
55 Healthy individuals
DGGE
qPCR
Joossens et al. (2011)
Faeces 16 CD patients (active disease)
16 Healthy individuals
qPCR
Phylogenetic microarray (16S)
Mondot et al. (2011)
Biopsies: inflamed and non-inflamed tissue (ileum, ascending/transverse/descending/sigmoid colon, rectum) 12 CD patients (active disease)
6 UC patients (active disease)
5 Non-IBD controls
qPCR
Clone library sequencing (16S)
Walker et al. (2011)
  1. Most of the studies used the Crohn’s disease activity index (CDAI; for CD) and/or the clinical activity index (CAI; for UC patients) to assess disease activity in the subjects and to define active disease or remission. Studies that have used subjects from the same cohort are indicated by *, # and †
  2. DGGE denaturing gradient gel electrophoresis, FISH fluorescence in situ hybridisation, HPLC high-performance liquid chromatography, qPCR quantitative polymerase chain reaction, RISA ribosomal intergenic spacer analysis, SSCP single strand conformation polymorphism, T-RFLP terminal-restriction fragment length polymorphism, TGGE temperature gradient gel electrophoresis