Systems Biology Assessment and Transcriptome Analysis of the Interaction of Probiotic and Host in the Anti-Inflammatory Process

Inflammatory diseases in the gut are linked with high levels of inflammatory oxidants, including hydrogen peroxide (H۲O۲) and hypochlorous acid (HOCI), which are antimicrobial compounds. Probiotics’ effectiveness in treating inflammation in the intestine depends on their ability to survive against H۲O۲ and HOCI stresses. In this study, by using the bioinformatics approach and the RNA sequencing data, the essential genes and pathways of resistance to H۲O۲ and HOCl stress in Lactobacillus reuteri (L. reuteri) was evaluated and investigated. After checking the GEO and SRA databases, the data related to L. reuteri (GSE۱۲۷۹۶۱) was retrieved, containing a probiotic under H۲O۲ and HOCI oxidative stress compared to control group (without oxidative stress). The data was analyzed by CLC software. After obtaining the di↵erentially expressed genes, analyzes were performed, such as investigating the gene/protein interaction network, extracting key genes, and finally evaluating the biological pathways and ontology of these genes. Based on the results, the GSE۱۲۷۹۶۱ related to L. reuteri (HOCI and H۲O۲ stresses) respectively, ۶۴ and ۱۹۸ DEGs were obtained. According to the results, deoC, mfd, uvrB and grpE genes in HOCI stress and Lreu ۰۶۴۵ gene in H۲O۲ stress are considered as key genes that probably play an essential role in the resistance of these probiotics to HOCI and H۲O۲ stress. Also, these key genes play a role in biological pathways such as ”homologous recombination”, ”mismatch repair”, ”nucleotide excision repair”, and ”pentose phosphate pathway” in stress conditions. The e↵ectiveness of probiotics in the host depends on their resistance and survival against oxidative stress such as H۲O۲ and HOCI. Therefore, the key genes and biological pathways obtained in this study can be used to improve probiotics’ e cacy in treating inflammatory diseases.

کلیدواژه ها:

Intestinal inflammation ، Probiotics ، Transcriptome ، Lactobacillus reuteri ، Resistance