Transcriptional profiling of biofilms formed on chilled beef by psychrotrophic meat spoilage bacterium, Pseudomonas fragi 1793

Pseudomonas fragi is the predominant bacterial species associated with spoiled aerobically stored chilled meat worldwide. It readily forms biofilms on meat under refrigerated temperature conditions used in the meat industry. Biofilm growth leads to slime development on meat which in turn becomes a major quality defect. To understand the genetic regulation that aids P. fragi to survive under chilled conditions used in the meat industry, as well to obtain an overview of the transcriptomic behavior of this organism when grown as biofilms, RNA sequencing was carried out for the main stages of the P. fragi 1793 biofilm. RNA was extracted at different stages of the biofilm cycle namely initiation, maturation and dispersal. At the same time, the biofilm growth was assessed by fluorescent staining and imaging using confocal laser scanning microscope. The results of RNA sequencing were verified by qRT-PCR using twelve genes that were most significantly up and down regulated at each stage. Differential expression analysis at biofilm maturation revealed 332 significantly upregulated genes and 37 downregulated genes relative to initiation. Differential expression analysis at biofilm dispersal reveled 658 upregulated and 275 downregulated genes relative to initiation. During biofilm maturation and dispersal, genes coding for flp family type IVb pilin, ribosome modulation factor, creatininase were the most upregulated genes while genes encoding for iron uptake systems including TonB-dependent siderophore receptor and taurine transport were significantly down regulated. The results show that protein synthesis and cellular multiplication cease after the biofilm population maximum has reached.