Discovery of a protective, transmissible, and type 2 inflammation-skewing intestinal microbiome

We recently discovered a transmissible, dominant, and remarkably protective intestinal microbiome (a “Magical Microbiome,” MM) in the setting of a murine model of colitis. The objective of this project is to fill current knowledge gaps regarding the molecular mechanisms underlying protection in this novel model of microbiome-mediated protection. Protection can be transmitted to unmanipulated conventional or germ-free C57Bl/6 mice via cohousing or oral gavage of MM+ stool. During DSS-induced colitis, MM+ mice develop less weight loss, intestinal pathology, and production of proinflammatory molecules relative to genetically identical C57Bl/6 MM-controls. Preliminary results suggest that the eukaryotic and bacterial microbiome under investigation re-programs the host inflammation to prevent disease or promote repair. MM-mediated protection is IL-13-dependent and associated with enhanced type 2 inflammation, as transcript levels of type 2-associated genes including IL-4, IL-13, and Fizz1 were significantly higher in colons of MM+ mice. 16s rRNA gene sequencing and eukaryote screening demonstrated that MM+ mice have a bacterial microbiome distinct from controls and host a novel Tritrichomonas species. Transfer of Tritrichomonas to wild-type mice correlated with protection, but vancomycin treatment ameliorates the protection while maintaining Tritrichomonas, suggesting a possible interaction between bacteria and protist. Stool metabolites are also distinct between MM+ and MM− hosts, further supporting a distinct microbiome function. Overall, we possess a unique microbiome that can be used to understand protective host-microbe interactions and identify novel therapeutic targets for inflammatory diseases.