Gene Networks Analysis of Salmonella Typhimurium Reveals New Insights on Key Genes Involved in Response to Low Water Activity.

Background: When Salmonella enterica serovar Typhimurium, a foodborne bacterium, is exposed to osmotic stress, cellular adaptations increase virulence severity and cellular survival.

Objectives: The aim of the gene network analysis of S. Typhimurium was to provide insights into the various interactions between the genes involved in cellular survival under low water activity (a_w).

Materials and methods: We performed a gene network analysis to identify the gene clusters and hub genes of S. Typhimurium using Cytoscape in three food samples subjected to a_w stress after 72 hours.

Results: The identified hub genes of S. Typhimurium belonged to down-regulated genes and were related to translation, transcription, and ribosome structure in the food samples. The rpsB and Tig were identified as the most important of the hub genes. Enrichment analysis of the hub genes also revealed the importance of translation and cellular protein metabolic processes. Moreover, the biological process associated with organonitrogen metabolism in milk chocolate was identified. According to the KEGG pathway results of gene cluster analysis, cellular responses to stress were associated with RNA polymerase, ribosome, and oxidative phosphorylation. Genes encoding RNA polymerase activity, including rpoA, rpoB, and rpoZ, were also significantly identified in the KEGG pathways. The identified motifs of hub DEGs included EXPREG_00000850, EXPREG_00000b00, EXPREG_000008e0, and EXPREG_00000850.

Conclusion: Based on the results of the gene network analysis, the identified hub genes may contribute to adaptation to food compositions and be responsible for the development of low water stress tolerance in Salmonella. Among the food samples, the milk chocolate matrix leads to more adaptation pathways for S. Typhimurium survival, as more hub genes were down-regulated and more motifs were detected. The identified motifs were involved in carbohydrate metabolism, carbohydrate transport, electron transfer, and oxygen transfer.