Streptococcus alactolyticus confers colonization resistance against Salmonella by enhancing intestinal barrier integrity and moderating host inflammation in chicks

Salmonella Enteritidis poses a persistent threat to poultry production and public health. While gut microbiota (GM) is known to influence host resistance, the precise microbial and host genetic factors that confer protection remain poorly defined. This study aims to systematically dissect the interaction mechanisms among host genetic variations, specific gut microbes, and immunomodulatory metabolites, elucidating the genetic basis by which they jointly drive colonization resistance against Salmonella in chicks. Using a controlled infection model in chickens, we established a phenotypic colonization resistance (CR) index and identified distinct resistant and susceptible cohorts. Resistant chicks exhibited higher abundances of Streptococcus alactolyticus ( S. alactolyticus ). Dietary supplementation with S. alactolyticus reduced Salmonella load and enhanced intestinal mucosal integrity in challenged birds. Transcriptomic and serum metabolomic analyses ( S. alactolyticus vs PBS) showed that at 6 h post- Salmonella infection, differentially expressed genes were significantly enriched in the TGF-β signaling pathway, while differential metabolites were mainly enriched in energy metabolism pathways such as the TCA cycle. A genome-wide association study (GWAS) identified a locus on chromosome 2 that was significantly associated with S. alactolyticus abundance. Integrated with transcriptomic analysis, PDK4 was pinpointed as the leading candidate gene. This study describes the host genetic, metabolic regulatory, and gut microbiota factors that control Salmonella resistance in chickens, in which PDK4 may influence Salmonella colonization through modulation of S. alactolyticus . Our findings highlight novel pathways for enhancing disease resistance through targeted manipulation of gut microbiota and host genetics.