Dairy propionibacteria are GRAS beneficial microorganisms, consumed within Swiss-type cheeses and probiotic food supplements. They are symbiotic members of the human gut microbiota. Their main recognized effect consists in the modulation of the immune response. In a strain-dependent manner, they induce the modulatory cytokine IL-10 in leukocytes, down-regulate inflammation in colonocytes, and prevent colitis in mice. We sought to identify the propionibacterial compounds involved in such a modulatory effect. We thus selected 25 strains of Propionibacterium freudenreichii with varied anti-inflammatory properties and sequenced their genomes. Comparative genomics led to a list of genes positively correlated with IL-10 induction. Comparative transcriptomic led to a list of correlated RNA tanscripts. An original surface proteomic comparative approach to a list of correlated surface proteins. Thus, comparative omics stressed out candidate genes, further subjected to gene inactivation. Two surface proteins, SlpB and SlpE, were shown to play a key role in immunomodulation. Inactivation of the slpB gene drastically modified P. freudenreichii surface properties (hydrophobicity, electronegativity) and abolished its ability to adhere to colonocytes. The obtained mutant failed to prevent both mucositis and colitis in mice, by contrast with the WT parental strain. Finally, heterologous expression of slpB in Lactococcus lactis conferred an ability to prevent colitis. These results strongly confirm the key role of SlpB in the probiotic effects of P. freudenreichii and open new perspectives for the development of probiotic and post-biotic products.