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Pathogen control is a critical issue in the layer industry. Plant-based natural products are firmly replacing the undesirable use of antibiotics in animal production. The poultry industry embraced the opportunity to distance itself from the negative public perception of antibiotic use. In this study, we investigated the effects of a phytogenic product comprising of menthol, carvacrol and carvone on ileum gene expression profile in layers after 16 weeks of continual supplementation. Phytogen supplementation increased endocytosis and autophagy while showing significant predicted cardiovascular protective effects. Statistical comparison with over 100,000 manually curated and comparably reanalysed public datasets suggests that the phytogen effects are highly significantly comparable with transcriptomic effects of clinical antibiotics doxycycline and geldanamycin, and that phytogen can reverse transcriptomic effects of a range of viral diseases and malaria. Our data confirmed the hypothesis that similarly to the original essential oil type antimicrobial constituents of phytogenic products, there may be a range of benefits unrelated to their critical antimicrobial action, contributing to improved bird welfare.