Besides the inconsistent results and inconclusive mechanisms, the challenges of using phytogenic compounds in animal feed may also include side effects, regulatory obstacles and cost-effectiveness. Nevertheless, application of novel technologies integrating research to simultaneously examine genomes, metagenomes, transriptomes and proteomes should help to better understand the modes of action of phytogenic compounds and subsequently lead to the development of feasible and cost-effective ways to use phytogenic compounds in animal feed.