Identification and Characterization of Immune-Associated MicroRNAs in Silver Carp (Hypophthalmichthys molitrix) Responding to Aeromonas veronii and LPS Stimulation

Infections caused by pathogenic bacteria are one of the main problems in silver carp (Hypophthalmichthys molitrix) aquaculture, resulting in elevated mortality rates and substantial economic losses. Therefore, it is of great significance to investigate the response of silver carp to pathogenic bacterial infection and its underlying regulatory mechanisms. MicroRNAs (miRNAs) play an important role in regulating the immune response of teleost fish. In this study, we established an inflammatory model in silver carp and employed bioinformatics analysis to identify miRNAs with immunomodulatory effects. The data obtained from this study lay a solid foundation for elucidating the regulatory function of silver carp miRNAs during bacterial infection, while also providing valuable insights into the molecular mechanisms governing miRNA adaptation in teleost fish during pathogen invasion. The ubiquitous Gram-negative bacterial pathogen Aeromonas veronii (A. veronii) can easily cause inflammatory reactions in aquatic organisms, resulting in high mortality and huge economic losses. MicroRNAs (miRNAs) participate in immune regulation and have certain conserved properties. MiRNAs are involved in the immune responses of a variety of teleost fish infected with bacteria, whereas there is no related report in silver carp (Hypophthalmichthys molitrix). Therefore, we identified the expression profiles of miRNA in silver carp stimulated by A. veronii and LPS. Among them, the quantity of differentially expressed miRNAs (DEmiRNAs) obtained in the silver carp challenge group was 73 (A. veronii) and 90 (LPS). The GO enrichment and analysis of KEGG pathways have shown that the predicted target genes are mainly associated with lipid metabolism and the immune response in silver carp. This indicates the possibility that miRNAs play a role in regulating immune-related pathways. In addition, a total of eight DEmiRNAs validated the accuracy of the sequencing result via quantitative real-time PCR (qRT-PCR). Finally, we selected the silver carp head kidney macrophage cells (HKCs) as model cells and proved that miR-30b-5p can regulate the inflammatory response in silver carp HKCs. This study lays the foundation for exploring miRNA regulation in silver carp during pathogenic bacterial infection. In addition, it provides a reference for the future development of non-coding RNA antibacterial drugs.