Gene expression in the chicken liver following vaccination and intravenous challenge. Upper panel, Principal Component Analysis (PCA) of individual chickens using “integrated” expression of 13 genes used for the characterization of chicken response to S. Enteritidis challenge. The chickens vaccinated with the vaccine mixed with probiotics responded to the infection similarly as the non-vaccinated chickens indicating their lowest level of protection. On the other hand, aerosol vaccinated chickens clustered the closest to the non-infected controls indicating the highest level of protection against intravenous challenge. Con: control, non-vaccinated and non-infected chickens, Inf: non-vaccinated but infected chickens, Or: orally vaccinated and infected chickens, OrP: orally vaccinated together with administration of cecal microbiota (probiotics) and infected chickens, Aer: aerosol vaccinated and infected chickens. Lower row of four panels, average expression of four genes with the highest expression in the chicken cecum following oral infection with S. Enteritidis. AVD: avidin, ExFABP: extracellular fatty acid binding protein, SAA: serum amyloid A, PTGDS: Prostaglandin D2 synthase. For the expression of all individual genes, see Additional file 1. * significantly different from non-vaccinated chickens but infected chickens by ANOVA at P < 0.05.