Fig. 1

Overview of the workflow by integrating multi-omics including host genes, intestinal microbes, and intestinal microbial genes. A Experimental design for selective breeding of the V. harveyi resistant and susceptible families in C. semilaevis. The selective breeding was performed for successive 4–5 generations over 10 years. The family having a survival rate > 80% and < 30% was considered as a V. harveyi resistant family and susceptible family, respectively. B The transcriptomic analysis of C. semilaevis genes in the resistant and susceptible families. C Profiling of the intestinal microbial communities for the resistant and susceptible families. D The functional analysis includes virulent factors (VFs), antibiotic-resistant genes (ARGs), and the KEGG pathway for intestinal microbial genes. E The association analysis of the host’s differentially expressed genes (DEGs) and intestinal microbes. The DEGs with |log₂(FoldChange)| > 1 and the adjusted p < 0.05, as well as the microbes with relative abundance > 0.1% and coverage of > 10% samples were selected for this association analysis. F Metabolism pathway enrichment analysis by integrating host genes, intestinal microbes, and intestinal microbial genes. G The prediction power of intestinal microbial markers, host functional markers, and their combinatorial markers in discriminating the resistant family from the susceptible family for C. semilaevis