Lysozyme and inulin are known to eliminate intestinal pathogens in poultry and improve their growth performance. However, whether they can replace antibiotic growth promoters without the associated risk of the emergence of antibiotic-resistant bacterial strains is not known, and the effects of lysozyme and inulin supplementation on the metabolism of the chicken gut microbiota remain unclear. Here, we used transcriptomic analysis to address this issue.