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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