This study investigates the microbial community imbalances in human inflammatory bowel diseases (IBD), specifically Crohn's disease (CD) and ulcerative colitis (UC), using a culture-independent rRNA sequence analysis of gastrointestinal (GI) tissue samples. The researchers obtained surgical specimens from a variety of intestinal sites, including both pathologically normal and abnormal states, from CD and UC patients, as well as non-IBD controls. The results provide a comprehensive molecular-based analysis of the microbiota in the human small intestine. Comparison of clone libraries reveals significant differences between the microbiotas of CD and UC patients and those of non-IBD controls. Notably, a subset of CD and UC samples showed abnormal GI microbiotas characterized by a depletion of commensal bacteria, particularly members of the phyla *Firmicutes* and *Bacteroidetes*. Patient stratification by GI microbiota suggests that CD represents a spectrum of disease states and indicates that treatment of some forms of IBD may be facilitated by addressing these detected microbiological imbalances. The study highlights the importance of understanding the role of gut microbes in IBD pathogenesis and provides insights into potential therapeutic targets.This study investigates the microbial community imbalances in human inflammatory bowel diseases (IBD), specifically Crohn's disease (CD) and ulcerative colitis (UC), using a culture-independent rRNA sequence analysis of gastrointestinal (GI) tissue samples. The researchers obtained surgical specimens from a variety of intestinal sites, including both pathologically normal and abnormal states, from CD and UC patients, as well as non-IBD controls. The results provide a comprehensive molecular-based analysis of the microbiota in the human small intestine. Comparison of clone libraries reveals significant differences between the microbiotas of CD and UC patients and those of non-IBD controls. Notably, a subset of CD and UC samples showed abnormal GI microbiotas characterized by a depletion of commensal bacteria, particularly members of the phyla *Firmicutes* and *Bacteroidetes*. Patient stratification by GI microbiota suggests that CD represents a spectrum of disease states and indicates that treatment of some forms of IBD may be facilitated by addressing these detected microbiological imbalances. The study highlights the importance of understanding the role of gut microbes in IBD pathogenesis and provides insights into potential therapeutic targets.