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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 in most cases. 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 of the spleen under the influence of host-microbiome interaction.    Results  Fertilized eggs of two genotypes: Ross 308 and Green-legged Partridgelike were  in ovo  stimulated on d 12 of incubation. The injected compounds were as follows: probiotic –  Lactococcus lactis  subsp . cremoris  IBB477, prebiotic – galactooligosaccharides, and synbiotic – combination of both. Chickens were sacrificed on d 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.

Interaction between early in ovo stimulation of the gut microbiota and chicken host – splenic changes in gene expression and methylation