COMPARATIVE ANALYSIS OF GUT MICROBIAL DIVERSITY IN HEALTHY INDIVIDUALS AND PATIENTS WITH INFLAMMATORY BOWEL DISEASE
Abstract
Gut microbial dysbiosis is common in inflammatory bowel disease (IBD), such as Crohn's disease and ulcerative colitis. This study aimed to compare the diversity and composition of the gut microbiome of healthy people and those with IBD. Shotgun metagenomic data that have been publicly made available from the Human Microbiome Project 2 IBD Multi-omics Database were analysed. After removal of duplicates, 1,373 stool samples from 116 individuals (27 healthy, 56 Crohn's patients, and 33 ulcerative colitis patients) were retained. Shannon index, Simpson index, inverse Simpson and observed species were used to assess alpha diversity. Differences among microbial communities were determined using Bray–Curtis dissimilarity, principal coordinate analysis, PERMANOVA and differential-abundance testing. Observed species richness was significantly higher in healthy subjects compared to those with IBD, with a median of 50 species and 40 species, respectively (p = 0.003). There were no significant differences between Shannon, Simpson or inverse Simpson indices across diagnostic groups. The beta diversity analysis revealed that there were significant overlaps among the groups, and the diagnostic model accounted for just 1.8% of the community variation (p = 0.395). The taxa Ruminococcus bicirculans, Gemmiger formicilis and Coprococcus eutactus were depleted in IBD while the taxa Flavonifractor plautii and Clostridium symbiosum were increased. Only Roseburia sp. The CAG 182 was still significant even after correction for the false discovery rate. IBD was mainly correlated with a decrease in microbial richness and taxon-specific changes, yet there was significant microbiome inter-personal diversity.
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