In the current study, the expression of the miR-339-5p target gene HTRA3 was down-regulated in the SR and SS groups compared to the SC group, although it was particularly higher in the SS group, after the piglets were infected with C. perfringens type C. This result indicated that the down-regulation of HTRA3 could increase the piglets’ immunity and resist the infection of C. perfringens type C. TNFAIP8L2 is a member of the tumor necrosis factor–alpha-induced protein 8 (TNFAIP8) family [41,42]. This evidence concerns the gene TNFAIP8 and infection.