Table 1. Studies on changes in intestinal microbiota composition associated with inflammatory bowel disease.
| Study | Disease | Sample material | Methods | Major results | Ref. |
|---|---|---|---|---|---|
| Swidsinski et al., 2008 |
CD, UC |
Feces |
FISH |
Depletion of F. prausnitzii in CD |
11 |
| Ott et al., 2004 |
CD, UC |
Mucosa |
16S rRNA gene clone libraries, SSCP, qPCR |
Reduced microbiota diversity; depletion of Bacteroides spp, Eubacterium spp, Lactobacillus spp |
14 |
| Nishikawa et al., 2009 |
UC |
Mucosa |
T-RFLP |
Reduced microbiota diversity; depletion of members of the clostridial closter XIVa |
15 |
| Frank et al., 2007 |
CD, UC |
Mucosa |
16S rRNA gene clone libraries |
Depletion of Bacteroidetes and Lachnospiraceae; relative increase in proteobacteria |
16, 17 |
| Andoh et al., 2007 |
UC |
Feces |
T-RFLP |
Presence of Ruminoccus spp, Eubacterium spp, Fusobacterium spp, Bacteroides spp, Lactobacillus spp, and proteobacteria which are absent in healthy controls |
18 |
| Andoh et al., 2012 |
CD |
Feces |
T-RFLP |
Depletion of the genera Faecalibacterium and Bifidobacterium; increase of the genus Bacteroides |
19 |
| Manichanh et al., 2006 |
CD |
Feces |
DNA clone library, FISH |
Reduced diversity within the Firmicutes |
20 |
| Willing et al., 2010 |
CD, UC |
Feces |
Pyrosequencing |
Depletion of Faecalibacterium and Roseburia; increased Enterobacteriaceae and Ruminococcus gnavus in CD |
22 |
| Walker et al., 2011 |
CD, UC |
Mucosa |
16S rRNA gene clone libraries |
Reduced microbiota diversity; depletion of Firmicutes.; increased Bacteroidetes (CD and UC) and Enterobacteria (CD) |
24 |
| Joossens et al., 2011 |
CD |
Feces |
DGGE, qPCR |
Depletion of butyrate-producing bacteria |
25 |
| Sokol et al., 2009 |
CD, UC |
Feces |
qPCR |
Depletion of Faecalibacterium prausnitzii |
26 |
| Sokol et al., 2008 |
CD |
Mucosa |
FISH |
Depletion of Faecalibacterium prausnitzii |
27 |
| Baumgart et al., 2007 |
CD |
Mucosa |
16S rRNA clone libraries, qPCR, FISH, characterization of E. coli isolates |
Depletion of Clostridiales; increase of invasive E. coli strains |
30 |
| Martin et al., 2004 |
CD, UC |
Mucosa |
Culture-based analysis; characterization of E. coli isolates |
Important role of adherent E. coli in CD |
31 |
| Martinez-Medina et al., 2009 |
CD |
Mucosa |
qPCR; characterization of E. coli isolates |
High abundance of AIEC |
32 |
| Sasaki et al., 2007 |
CD, UC |
Mucosa |
characterization of E. coli isolates |
Important role of invasive E. coli in CD |
33 |
| Darfeuille-Michaud et al., 1998 |
CD |
Mucosa |
characterization of E. coli isolates |
Important role of adherent E. coli in CD |
34 |
| Darfeuille-Michaud et al., 2004 |
CD, UC |
Mucosa |
characterization of E. coli isolates |
Important role of invasive-adherent E. coli in CD |
36 |
| Swidsinski et al., 2005 |
CD, UC |
Mucosa |
FISH |
Important role of B. fragilis |
43 |
| Seksik et al., 2003 |
CD |
Mucosa |
Dot blot hybridization |
Increased Enterobacteria |
45 |
| Kotlowski et al., 2007 | CD, UC | Mucosa | characterization of E. coli isolates | High abundance of E. coli with potentially pathogenic traits | 47 |
Abbreviations used: CD, Crohn’s Disease; UC, ulcerative colitis; DGGE, denaturing gradient gel electrophoresis; FISH, fluorescence in situ hybridization; qPCR, quantitative PCR; SSCP, single strand conformation polymorphism; T-RFLP, terminal restriction fragment length polymorphism.