Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn's Disease: Results from the IMPACT Study

Limited studies have examined the intestinal microbiota composition in relation to Crohn's disease (CD) prognosis. We analyzed the differences in microbial communities and relevant metabolic pathways associated with prognostic variables in patients with CD. We applied 16S rRNA gene sequencing to analyze a cohort of 1110 CD and healthy control (HC) fecal samples. We categorized patients with CD into good (CD-G), intermediate (CD-I) and poor (CD-P) prognosis groups, according to the history of using biologics and intestinal resection. Microbiota alpha-diversity decreased more in CD-P than CD-G and CD-I. Microbiota ss-diversity in CD-P differed from that in CD-G and CD-I. Thirteen genera and 10 species showed differential abundance between CD-G and CD-P groups.Escherichia coli(p= 0.001) and speciesProducta(p= 0.01) and generaLactobacillus(p= 0.003) and Coprococcus (p= 0.01) consistently showed differences between CD-G and CD-P groups after adjusting for confounding variables. Functional profiling suggested that the microbial catabolic pathways and pathways related to enterobacterial common antigen and lipopolysaccharide biosynthesis were better represented in the CD-P group than in the CD-G group, andE. coliwere the top contributors to these pathways. CD prognosis is associated with altered microbiota composition and decreased diversity, andE. colimight be causally involved in CD progression, and may have adapted to live in inflammatory environments.