Dual Salmonella vaccination attenuates microbiota dysbiosis and enhances microbiota functionality in poultry challenged with S. Typhimurium

Salmonella is a leading cause of gastrointestinal illness and foodborne outbreaks worldwide, with poultry products such as eggs as the primary source of infection. In this context, live attenuated vaccines play a critical role in reducing the risk of infection in poultry flocks. However, their impact on the gut microbiota remains poorly understood. Thus, the aim of this study was to evaluate the effects of a live attenuated combined vaccine against Salmonella Enteritidis and Salmonella Typhimurium on the gut microbiota of chicks challenged with S. Typhimurium, including the study of microbial balance and functionality. The trial involved 40 specific pathogen-free chicks, divided into vaccinated and control groups, all challenged with S. Typhimurium at 14 days of age. Afterwards, caecal content of 10 animals per group was collected at 7 and 14 days post infection. Then, the composition, diversity and functionality of the microbiota were analyzed using 16S rRNA sequencing and bioinformatic analysis. The results of the taxonomic analysis revealed 1,261 bacterial taxa, with Firmicutes and Proteobacteria as the dominant phyla. In addition, vaccination resulted in significant changes in microbiota composition, with marked differences in microbial diversity between groups. PLS-DA and Bayesian analysis identified key species such as Clostridium innocuum in vaccinated chicks and Eubacterium coprostanoligenes in the control group. Results also showed that vaccination promoted the growth of beneficial genera such as Lactobacillus and Blautia, which was associated with reduced Salmonella colonization and shedding. Alpha diversity analysis revealed significantly higher microbial richness and evenness in the control group. Finally, functional annotation revealed shared microbial functions between the groups, with potentially pathogenic bacteria, including Salmonella, present in both. These results suggest that vaccination improves microbiota stability and supports the protective role of beneficial bacteria against Salmonella, highlighting the importance of vaccination in improving poultry health and pathogen control throughout the food chain.