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Slow-growing breeds are more resistant to Salmonella infection compared to fast-growing broilers. However, it is unclear whether that is associated with innate resistance or rather rely on differences in Salmonella-induced gut responses. We investigated the microbial composition and gene expression of nutrient transporters, mucin, and interleukin in the gut of a fast-growing (Cobb500) and a slow-growing naked neck (NN) chicken breeds challenged with Salmonella Enteritidis. Hatchlings were inoculated at two days of age using sterile broth (sham) or Salmonella Enteritidis (SE) and distributed according to a completely randomized design into four treatments: Cobb-sham; Cobb-SE; NN-sham; and NN-SE. Cecal SE counting and microbial composition by 16 S rRNA sequencing were determined at 24-, 96-, and 168-hours post-inoculation (hpi). Gene expression of amino acid (Asct1) and peptide transporters (PepT1), glucose transporters (Sglt1, Glut2 and Glut5) and mucin (Muc2) in the jejunum and expression of interleukins (IL1 beta, IL8, IL17 and IL22) in the cecum was assessed by qPCR at 24 and 168 hpi. NN birds were colonized by SE just as Cobb birds but showed innate upregulation of Muc2, IL8 and IL17 in comparison to Cobb. While nutrient transporter mRNA expression was impaired in SE-challenged Cobb birds, the opposite was observed in NN. There were no differences in microbial diversity at different sampling times for Cobb-SE, whereas the other groups had higher diversity and lower dominance at 24 hpi compared with 96 hpi and 168 hpi. NN birds apparently develop earlier gut microbial stability, have higher basal level of mucin gene expression as well as differential nutrient transporter and interleukin gene expression in the presence of SE which might mitigate the effects of SE infection compared to Cobb birds., (© 2024. The Author(s) under exclusive licence to Sociedade Brasileira de Microbiologia.)