Gene expression in the chicken caecum following oral infection of newly hatched chickens. Genes dominantly expressed in the caecum of non-infected chickens are those associated with normal gut function, i.e. nutrient uptake. The first genes induced within 48 hours after the infection represent components of the innate immune system and chemokines. Induction of MMP7 results in tissue relaxation allowing for the infiltration of leukocytes. B cells are absent in the chicken caecum until day 7 of life, irrespective of infection. Ten days post-infection, cytokines modifying immune responses are expressed by T cells and macrophages, and heterophils, macrophages and B cells express proteins that facilitate Salmonella clearance. Heterophils furthermore express proteins (TRAP6 and SERPINB10) that protect chicken tissue against its own proteases. Proteins shown in the figure are placed close to the cell type which is the most important for their expression.