Background: Epigenetic regulation of the gene expression results from interaction between the external environment and transcription of the genetic information encoded in DNA. Methylated CpG regions within the gene promoters lead to silencing of the gene expression. Factors contributing to epigenetic regulation include intestinal microbiota, which in chicken can be potently modified by in ovo stimulation. The main aim of this study was to determine global and specific methylation patterns for

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... e spleen under the influence of host-microbiome interaction. Results: Incubating eggs were in ovo stimulated on day 12 of incubation in two chicken genotypes: Ross broilers and Green-legged Partridgelike. The injected compounds included: probiotic – Lactococcus lactis subsp. cremoris, prebiotic – galactooligosaccharides, and synbiotic – combination of both. Chickens were sacrificed on day 42 post-hatching. Spleen was collected, RNA and DNA were isolated and intended to gene expression, gene methylation and global methylation analysis. We have proved that negative regulation of gene expression after administration of bioactive substances in ovo might have epigenetic character. Epigenetic changes depend on the genotype and the substance administered in ovo. Conclusion: Epigenetic nature of microbial reprogramming in poultry and extension of issues related to host-microbiome interaction is a new direction of this research.