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To study changes in the intestinal flora associated with inflammatory bowel disease (IBD) in the Han population of southwest China, 48 participants were enrolled, 18 of whom had been diagnosed with IBD. Stool samples were collected from the participants. Sequencing of 16S rRNA gene was used to measure and identify the components of the intestinal flora. Diversity analysis and multivariate statistical analysis were conducted to study differences in intestinal flora between patients with IBD and healthy controls. The goods coverage, observed species, Shannon, and Simpson indices of alpha diversity were different (p < 0.05). Beta diversity analysis yielded significant differences between groups (R = 0.5668, p = 0.001 < 0.05). Compared with the composition of the intestinal flora in healthy controls, the relative abundances of Proteobacteria (18.56% vs. 3.56%, p = 0.001) and Fusobacterium (2.08% vs. 0.35%, p = 0.005) were higher in patients with IBD. Therefore, this study provides insight into the role of the microbiome in IBD. [ABSTRACT FROM AUTHOR]