mouse gut metagenome raw sequence reads. mouse gut metagenome

The colonic microenvironment, consisting of colonic epithelial cells, resident tissue immune cells, and commensal microbes, serves as an important determinant to how a host will respond to enteric pathogenic colonization. Infection with the enteric bacterial pathogen Citrobacter rodentium, a murine homolog to enteropathogenic Escherichia coli and enterohemorrhagic E. coli, elicits a strong mucosal Th1-mediated colitis that is attributed to monocyte-driven inflammation activated via the classical NF-κB pathway. Currently, research has focused on immune-mediated signaling as the main driver for C. rodentium-induced colitis; however, we hypothesize due to the intimate contact made between C. rodentium and colonic epithelial cells that NF-κB-derived, epithelial gene expression is also necessary for the exacerbation of infectious colitis. To test this hypothesis, compartmentalized classical NF-κB defective mice, via the deletion of IKKβ in either intestinal epithelial cells (IKKβΔIEC) or myeloid-derived cells (IKKβΔMY), and wild type (WT) mice were orally challenged with C. rodentium. Pathogen colonization and subsequent colonic histopathology were significantly reduced in IKKβ-deficient mice compared to WT mice, possibly due to a basal activation of non-classical NF-κB activation as evidenced by enhanced p52 activation in addition to increased colonic IL-10, RegIIIγ, TNF-α, and iNOS gene expression in IKKβ-deficient mice prior to bacterial challenge. The deletion of compartmentalized classical NF-κB also led to distinct changes in colonic tissue-associated and luminal bacterial populations, such as significant changes in tissue-associated Shannon and Chao1 alpha diversity and beta diversity. In each case of bacterial diversity IKKβ-deficient mice populations were distinct from that of WT mice. Taken together, these data indicate that classical NF-κB signaling in colonic epithelial cells and myeloid-derived cells can lead to enhanced enteric pathogen colonization and resulting colonic histopathology.