Abnormalities have been described in the fecal microbiota of patients with IBD, but it is not known whether they are specific for inflammatory bowel disease (IBD) or to some extent common to other forms of colitis. The aim of this study was to compare the bacterial composition of the dominant fecal microbiota in patients with Crohn's disease (CD), ulcerative colitis (UC), infectious colitis (IC), and in healthy subjects (HS). Methods: Fluorescent in situ hybridization adapted to flow cytometry was used to analyze the bacterial composition of fecal samples from 13 patients with active CD, 13 patients with active UC, 5 patients with IC, and 13 HS. We used 6 group-specific probes targeting 16S rRNA and spanning the main phylogenetic groups of the fecal microbiota. Results: A significantly higher proportion of the total fecal bacteria were recognized by the 6 probes in HS (86.6% +/- 12.7) and in IC (84.0% +/- 11.7) than in patients with IBD (70.9% +/- 15 in CD and 60.1% +/- 25.7 in UC). The Clostridium coccoides group was reduced in UC (20.0% +/- 13.3 versus 42.0% +/- 12.0 in HS; P < .001), whereas the C leptum group was reduced in CD (13.1% +/- 11.9 versus 25.2% +/- 14.2 in HS; P = .002). The Bacteroides group was more abundant in IC (36.4% +/- 22.9) than in the other 3 groups (13.8% +/- 11.8 in CD, 11.7% +/- 11.7 in UC, 12.1% +/- 7.0 in HS; P < .001 for all 3 comparisons). Conclusions: In IBD the dominant fecal microbiota comprises unusual bacterial species. Moreover, CD and UC fecal microbiota harbor specific discrepancies and differ from that of IC and healthy subjects.