Abstract
Microbiota-metabolized small molecules play important roles to regulate host immunity and pathogen virulence. Specifically, microbiota generates millimolar concentration of short-chain fatty acid (SCFA) that can directly inhibit Salmonella virulence. Here, we describe chemical proteomic methods to identify SCFA-modified proteins in Salmonella using free fatty acids as well as their salicylic acid derivatives. In addition, we include CRISPR-Cas9 gene editing protocols for epitope-tagging of specific proteins to validate SCFA-modification in Salmonella. These protocols should facilitate the discovery and functional analysis of SCFA-modified proteins in Salmonella microbiology and pathogenesis.