Iridoviruses are an important pathogen of ectothermic vertebrates and are considered a significant threat to aquacultural fish production. Recently, one of the most economically important marine species in China, the large yellow croaker (Larimichthys crocea), has been increasingly reported to be the victim of iridovirus disease. In this study, we isolated and identified a novel iridovirus, LYCIV-ZS-2020, from cage-cultured large yellow croaker farms in Zhoushan island, China. Genome sequencing and subsequent phylogenetic analyses showed that LYCIV-ZS-2020 belongs to the genus Megalocytivirus and is closely related to the Pompano iridoviruses isolated in the Dominican Republic. LYCIV-ZS-2020 enriched from selected tissues of naturally infected large yellow croaker was used in an artificial infection trial and the results proved its pathogenicity in large yellow croaker. This is the first systematic research on the genetic and pathogenic characterization of iridovirus in large yellow croakers, which expanded our knowledge of the iridovirus.

Various immunostimulants have been employed to enhance the efficacy of aquaculture. However, the mechanisms by which Eucommia ulmoides extracts affect the pathogen resistance of large yellow croakers remain to be elucidated. In this study, a multi-omics investigation was conducted to investigate the potential for enhancing pathogen resistance and to elucidate the underlying mechanisms of Eucommia ulmoides extracts on large yellow croaker juveniles. It revealed that the survival rate of the large yellow croaker juveniles was significantly enhanced (approximately doubled) by oral extracts of Eucommia ulmoides in the context of pathogen invasion. Examining the transcriptome of the liver revealed that Eucommia ulmoides extracts have the capacity to activate the class I MHC pathway for antigen processing, including genes for HSP70, HSP90, CALR, TAPBP, MHCI, and TCR. This, in turn, facilitates the phagocytosis of pathogens by the immune system. Furthermore, the alpha-diversity of the large yellow croaker juveniles’ gut microbiota was increased by the Eucommia ulmoides extracts, maintaining the stability of the gut microbiota and reducing the ratio of pathogens (Burkholderia cenocepacia and Streptococcus iniae) following a pathogen challenge. The application of correlation analyses indicated that a reduction in pathogens was closely associated with variations in whole gut microbiota.