Genotype-phenotype associated comparisons of Pseudomonas carnis spoilage ability based on whole-genome analyses

The Pseudomonasstrains as the key psychrotrophic bacteria in raw milk, could hydrolyze milk proteins and destroy milk stability via producing extracellular metalloproteases. However, the reasons for the variations in enzyme-producing capacity and spoilage potential among different Pseudomonas strains remain poorly understood. To explore the molecular mechanisms underlying varied spoilage ability among Pseudomonas spp., six Pseudomonas carnis from raw milk were performed whole-genome average nucleotide identity (ANI) analysis. Furtherly, combining core and unique gene analysis, sequence alignment of aprX and its promoter region, homology modeling, molecular docking, and protease activity assays. This study demonstrated the molecular basis of differential protease activities among strains. The results indicated that the protease-producing potential of Pseudomonas is associated not only with the promoter structure and key amino acid variations in its coding region, but also potentially associated with two-component systems, quorum sensing, and membrane function-related genes. These findings provide a candidate genomic basis for exploring the genetic mechanisms of protease activity variation in Pseudomonas strains of dairy products.