An RNA-seq analysis was conducted to compare the ETC-associated genes in ΔyqiC with those in S. Typhimurium SL1344 after 2 h of in vitro infection in Caco-2 cells: the analysis revealed that the depletion of yqiC significantly upregulated ndh, sdhA, and appB and caused upregulation trends for nuoA, sdhB, and cyoA; however, no significant regulation of nuoE, cyoC, or cydA was detected (Additional file 9: Table S9), indicating that a reverse regulation occurred after the interaction of S. Typhimurium with Caco-2 cells. This evidence concerns the gene SDHA and infection.