Gut microbiome-derived indoles differentially suppress type III secretion system-associated virulence in Escherichia coli and Salmonella enterica

Enteric pathogens such as enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and Salmonella enterica utilize a conserved type III secretion system (T3SS) to manipulate host cell processes and promote infection. Metabolites present in the intestinal lumen can directly influence the activity of these systems. Indole, which is produced from dietary tryptophan, has been shown to suppress the T3SS function of enteric pathogens. Here, we investigated the anti-virulence potential of seven gut microbiome-derived indole derivatives and found that their ability to suppress T3SS-dependent virulence is highly structure-dependent. Whereas indole exhibited moderate inhibition, indole-3-carboxaldehyde (I3A) and 3-methylindole (3-MI) emerged as more potent suppressors. In practice, these metabolites downregulated transcription of key T3SS genes, leading to reduced secretion of T3SS translocators, impaired effector delivery into host cells, and a marked reduction in actin pedestal formation, a hallmark of EPEC infection. Notably, this inhibitory effect extended to EHEC and Salmonella , suggesting that these metabolites target conserved virulence regulatory pathways. Overall, our findings demonstrate that microbiome-derived indole metabolites can effectively attenuate pathogen virulence. By targeting virulence rather than bacterial viability, 3-MI and I3A emerge as promising postbiotic-like therapeutic leads that can mitigate infection while limiting selective pressure for resistance.