PROJECT SUMMARY/ABSTRACT Dysregulated inflammation causes numerous diseases that impact millions worldwide. In concert with the human genome, gut bacteria of the microbiome regulate development and function of the immune system, modulating the balance between pro- and anti-inflammatory responses. A considerable body of evidence based on preclinical and clinical research suggests that gut microbes play a critical role in inflammatory bowel diseases (IBD), a family of idiopathic intestinal disorders with increasing prevalence and limited treatment options. Concordance rates of 30-40% among monozygotic twins in Crohn's disease (CD) implicate gene-environment interactions. Advances in DNA sequencing technologies have enabled detailed genomic characterization of IBD patients and controls, and numerous studies have chronicled changes in the composition and gene content of the microbiome during disease. Despite a wealth of sequence-based data, few hypothesis-driven studies have described molecular interactions between the microbiome and IBD-related genetic pathways. Genome-wide association studies (GWAS) and deep genomic sequencing have implicated roughly 200 susceptibility loci that are associated with IBD. Many variants encode for genes involved in microbial recognition and immunity, suggesting host-microbial interactions may regulate the balance between health and disease. Polymorphisms in genes of the autophagy pathway (e.g., ATG16L1), and in bacterial pattern recognition receptors that activate autophagy (e.g., NOD2), represent some of the most significant effect sizes in CD susceptibility. Further, considerable preclinical research has focused on investigating the function of ATG16L1 and NOD2 in mouse models and human cells, and identified a role for both factors in sensing and killing of infectious microbes. Conventional wisdom and current perspectives therefore suggest that CD may be caused by mutations that impair immunity to pathogenic bacteria, leading to chronic exposure to microbial products that promotes uncontrolled inflammation. Herein, we present new findings that beneficial gut bacteria require ATG16L1 and NOD2 to engender anti-inflammatory responses in mouse and human cells, and mice lacking these genes are not protected from experimental colitis by probiotics. Based on this discovery, we propose a novel, non-redundant role for genes previously implicated in recognition and killing of pathogenic bacteria— namely, mutations in genetic pathways linked to CD result in defective recognition of beneficial molecules from the microbiome. In other words, the absence of sensing and responding to anti-inflammatory bacterial signals due to defects in ATG16L1 and NOD2 leads to chronic intestinal inflammation. If validated, this innovative hypothesis will define novel functions for primary CD risk factors, embolden new research into understanding IBD etiology, and advance promising microbiome-based therapies for disease.