TDH and infection: To determine if T3SS2 and TDH have confounding effect, we used POR3 strain (both TDH and T3SS2 were mutated) as the parental strain in the culture infection assay, and the results showed that T3SS1 gene expression can be repressed in POR3, but not in POR3ΔvbrK (Supplementary Fig. 7e, f), consistent with the results when WT was used as parental strain (Fig. 6c–f), indicating that T3SS2 and TDH do not affect the ability of VbrK to sense nitrite and repress T3SS1 gene expression.