Systems Biology Evaluation and Transcriptome Analysis of Escherichia coliNissle ۱۹۱۷ in the Anti-Inflammatory Process

Background and Objective: High levels of inflammatory oxidants such as hypochlorous acid (HOCI),as an antimicrobial compound, are observed in inflammatory bowel diseases. An imbalance in thecomposition of intestinal microbiota occurs with the increase in the level of these inflammatory oxidants.According to various studies, probiotics are living organisms that are beneficial for people's health. Someprobiotics have an anti-inflammatory role in the body; In other words, in the digestive tract, they balancethe microbial flora and regulate the host's immune system. The effectiveness of probiotics in the intestineand the improvement of inflammatory diseases depends on their survival in dealing with oxidative stress;it is very important to study the path of reaction and resistance of different probiotics against stress. Inthis study, with the bioinformatics approach and the use of RNA-seq data, key genes and resistancepathways against HOCI stress were analyzed in the probiotic Escherichia coli Nissle ۱۹۱۷.Methods: The RNA-seq data related to the probiotic Escherichia coli Nissle ۱۹۱۷ (GSE۱۴۴۰۶۸) wasselected after reviewing and searching the GEO and SRA databases, which includes the probiotic exposedto HOCI oxidative stress compared to the non-stressed or control group. CLC Genomics Workbenchsoftware (version ۲۰۲۰) was used for relevant data analysis. Different steps of analysis include qualitycontrol of data, removal of low-quality reads, mapping of reads based on the reference genome, andobtaining differentially expressed genes (DEGs). Then the STRING database (version ۱۱.۵) was used toinvestigate the gene/protein interaction network of DEGs. Also, visualization of interactions extractedfrom STRING was done with Cytoscape ۳.۹.۱ software. Key genes were identified via the cytoHubbaplugin. Finally, by using STRING, the relationship between key genes and neighboring genes wasinvestigated and the biological pathways and ontology of these genes were studied.Results: According to the results, ۵۵۵ DEGs were obtained from the GSE۱۴۴۰۶۸ data related to theprobiotic Escherichia coli Nissle ۱۹۱۷. After extracting the gene/protein interaction network, two keygenes, guaA and tig, were obtained by using the cytoHubba plugin, which probably plays an importantrole in the resistance of this probiotic against HOCI stress. Also, the results revealed that these key genesare involved in biological pathways such as ribosome and purine metabolism.Conclusion: During inflammation, the immune system produces antimicrobial compounds such as HOCIas inflammatory oxidants. The benefits of probiotics depend on their ability to cope with oxidative stresssuch as HOCl in the host's body. Therefore, the key genes and biological pathways obtained in this studyprovide a general overview of how probiotics respond and resist stress and can be used to improve theeffectiveness of probiotics in the treatment of inflammatory diseases

کلیدواژه ها:

Escherichia coli Nissle ۱۹۱۷ ، Intestinal inflammation ، Probiotics ، Transcriptome