Salmonella Enterica Serovars Enteritidis Infection Alters the Indigenous Microbiota Diversity in Young Layer Chicks

Avian gastrointestinal tracts are highly populated with a diverse array of microorganisms that share a symbiotic relationship with their hosts and contribute to the overall health of the intestinal tract. The genetic background of the host and exposure to pathogens can impact the diversity of the microbial profile that consequently contributes to the disease progression in the host. The objective of this study was to examine the impact of host genetic background on influencing early establishment of microbiota in combination with S. Enteritidis infection to determine S. Enteritidis-associated alteration in gut microbiota with 16S rRNA sequencing analysis. One-day-old layer chicks were challenged with S. Enteritidis and the host microbiota profile as well as the degree of susceptibility to Salmonella infection was examined between two genetic lines at 2 and 7 days post-infection. Alpha diversity, beta diversity, and overall microbiota composition was analyzed for four factors: host genotype, age, treatment, and post-infection time-points. S. Enteritidis infection in young chicks were found to significantly reduce the overall diversity of the microbiota population with expansion of Enterobacteriaceae family. Significant inverse correlation between Enterobacteriaceae and Lachnospiraceae family in both non-infected and infected groups, suggested possible antagonistic interaction between members of these two taxa, which could potentially influences the overall gut microbial population. Our results also revealed that genetic difference between two genetic lines had minimal effect on the establishment of microbiota population. Overall, this study provided preliminary insights into the contributing role of S. Enteritidis in influencing the overall makeup of chicken's gut microbiota.