16S rRNA analysis of mouse gut microbiota (IBD-CDI)

The broad goal of this study was to disentangle the role of intestinal inflammation and associated in changes in the gut microbiota in modulating susceptibility to Clostridioides difficile infection (CDI) in the setting of IBD. We used a mouse model of IBD, in which colitis is triggered by colonizing IL-10-/- mice with the bacterium Helicobacter hepaticus. 16S rRNA amplicon sequencing was used to analyze the microbiota of mice without IBD as well as mice with H. hepaticus-triggered colitis and treated with a monoclonal antibody targeting the p40 subunit of the pro-inflammatory cytokines IL-12 and IL-23 (anti-p40) and colitic animals treated with a control antibody over time (i.e., before colitis, during peak colitis, and after antibody treatment/day of C. difficile challenge). Moreover, we aimed to better understand the specific role of the microbiota by completing fecal microbiota transfer experiments in wild-type germ-free mice using donor fecal material from colitic mice treated with control mAb or anti-p40 that were either susceptible or resistant to C. difficile.