RNA-Seq and Single-Cell RNA-Seq Analyses of Tilapia Head Kidney in Response to Streptococcus agalactiae and Aeromonas hydrophila

High-throughput sequencing has significantly advanced the exploration of fish immune mechanisms, enabling a more detailed understanding of immune responses and their underlying molecular pathways. In this study, we applied comparative transcriptomics and single-cell RNA sequencing to investigate the immune mechanisms of tilapia in response to different pathogenic bacteria. Our results demonstrated that nonspecific cytotoxic cells (NCCs) and monocytes/macrophages (Mos/Mφs) mounted the most pronounced responses to both <i>Streptococcus agalactiae</i> and <i>Aeromonas hydrophila</i> infections. Moreover, Mos/Mφs exhibited distinct differentiation patterns depending on the bacterial challenge. Collectively, these findings offer new insights into the antibacterial immune strategies of lower vertebrates.