Gut microbiota dysbiosis and predicted metabolic functional shifts associated with fowl typhoid in layer hens

Fowl typhoid (FT), caused by Salmonella enterica subsp. enterica serovar Gallinarum biovar Gallinarum, causes important health problems and economic losses in the poultry industry. In this study, we investigated the gut microbiota composition and predicted metabolic functions in 7-week-old layer hens infected with S. Gallinarum and compared with those of healthy counterparts. Taxonomic profiles were characterized using 16S rRNA gene (V3-V4 region) sequencing of fecal samples from naturally infected and healthy layer hens, and microbial metabolic functions were inferred using PICRUSt2. Disruption of the gut microbiota was observed in S. Gallinarum infected group marked by a significant decrease of beneficial bacteria (Lactobacillus and Enterococcus) and increase of potentially pathogenic bacteria (Bacteroides and Escherichia-Shigella). There was no significant difference in Chao1 index. But Shannon and Simpson indices were significantly lower in the healthy group compared to S. Gallinarum infected group, and beta diversity analysis (Bray-Curtis and Jensen-Shannon Divergence) showed a clear separation between two groups, indicating distinct microbial community structures. Also, pathways associated with amino acid biosynthesis, peptidoglycan maturation, and carbohydrate fermentation were predicted to be reduced in the S. Gallinarum infected group, suggesting differences in predicted microbial metabolic capacity. Through this, we found that S. Gallinarum infection was associated with compositional and functional dysbiosis in the gut microbiota of layer hens, potentially affecting intestinal homeostasis during the birds' early development. Understanding these changes provides valuable insights into the pathophysiology of FT, and supports the development of microbial community-based strategies to enhance the resilience of hosts.