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

Document Type : Research Paper


1 Department of Food Science and Technology, College of Food Industry, Bu-Ali Sina University, Hamedan, Iran

2 Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, Iran

3 Nutrition Research Center, Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran

4 Australian Red Cross Lifeblood, West Melbourne 3003, VIC, Australia 0000-0002-2442-8162


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 (aw).
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 aw 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 
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. 


Main Subjects

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