Navigating contradictions in enteric chemotactic stimuli

Previously, we showed Enterobacteriaceae use chemotaxis and the chemoreceptor Tsr for attraction to blood serum (Glenn et al., 2024). Here, we investigated the complementary role of Tsr in mediating chemorepulsion, a behaviour by which motile bacteria avoid deleterious compounds to locate permissive niches. In the gut, indole is a bacteriostatic compound produced by microbiota and thought to act as a chemorepellent for invading pathogens, thereby protecting the host against infection. The principal reservoir of intestinal indole is fecal matter, a complex biological material that contains both attractant and repellent stimuli. Whether indole in its natural context is sufficient for pathogen chemorepulsion or host protection has remained unknown. Using an intestinal explant system, we show that pure indole suppresses an infection advantage mediated through chemotaxis for the enteric pathogen Salmonella Typhimurium, but this effect is abolished in the presence of other fecal chemoeffectors, including the chemoattractant L-Serine (L-Ser), dependent on the chemoreceptor Tsr. Live imaging reveals that although S. Typhimurium is repelled by pure indole, the pathogen is actually strongly attracted to human fecal matter despite its high indole content, and this response is mediated by Tsr, which simultaneously senses both stimuli. Fecal attraction is conserved across diverse Enterobacteriaceae species that harbor Tsr orthologues, including Escherichia coli, Citrobacter koseri, Enterobacter cloacae, and clinical isolates of non-typhoidal Salmonella. In a defined system of fecal chemoeffectors, L-Ser and other fecal chemoattractants override indole chemorepulsion, but the magnitude of bacterial chemoattraction is controlled by indole levels. Together, these findings suggest chemorepulsion elicited by indole is not protective against enteric infection and actually benefits pathogens by helping them locate niches with lower competitor density. Our study highlights the limitations of applying single-effector studies in predicting bacterial behavior in natural environments, where chemotaxis is shaped by the integration of multiple, often opposing, chemical signals.