B. amyloliquefaciens TL acts on broiler ileum tissues and significantly downregulates immune-related genes in the “cytokine–cytokine receptor interaction” pathway. (a) “cytokine–cytokine receptor interaction” pathway. The genes in the green boxes represent genes expressed in birds, and the genes in the purple box represent the downregulated genes related to immune activity obtained in this study. (b) Schematic diagram of the function of the cytokine or cytokine receptor encoded by the downregulated gene. The interaction between the chemokine CXCL13 and its sole receptor CXCR5 guides B cells to B cell follicles and participates in the zoning of germinal centers. It also attracts T cells to B cell areas and mediates the interaction between B and T cells [66]; the interaction of BAFF and its receptor BAFFR (encoded by TNFSF13C) plays a central mediator in the homeostasis of mature B cell subsets, mainly through the modulation of cell survival. Unlike mammals, BAFF is also involved in early B cell development in birds [68]; the interaction of IL-8 with IL8RA, a G-protein-coupled receptor is responsible for the activation of neutrophils. An IL-8-activated neutrophil is characterized by enhanced migration, phagocytosis, superoxide generation, and granule release [60]; IFN-γ interacts with its receptor IFNGR1, activates type I macrophages, enhances the activation of both MHC-I and MHC-II molecules, and assists in antigen presentation and processing, as well as removal of intracellular pathogens, and prevents virus replication. Moreover, IFN-γ activates T-helper I-type immune responses [70]; the chemokine CCL19 interacts with its receptor CCR7 and plays a pivotal role in T cell and dendritic cell trafficking into Bursa of Fabricius and other lymphoid tissues [76]. B. amyloliquefaciens TL acts directly or indirectly (indicated by the pink dotted arrow in the figure) on immune cells to reduce the expression of corresponding cytokines or cytokine receptors, thereby downregulating the above-mentioned immune activity and reducing the energy consumption of immune activation, which is beneficial for the accumulation of energy in broilers.