Interactions between the intestinal microbiome and host genes in regulating vibriosis resistance in Cynoglossus semilaevis

Chinese tongue sole (Cynoglossus semilaevis) is now a commercially important and widely farmed flatfish species in China. In recent years, due to the frequent outbreak of vibriosis, it has caused high mortality rate and serious economic losses to the breeding industry of Chinese tongue sole. Intestinal microbiome plays important roles in host immunity, and protection against pathogen invasion. However, the interactions between the intestinal microbiome and host genes in vibriosis are poorly understood. In this study, we investigated the changes in the intestinal histopathology, microbiome and host gene expression in resistant and susceptible individuals of Chinese tongue sole after infection with Vibrio harveyi for 7 days, and identified the host gene-microbe correlations. Obvious histopathological differences were detected in resistant and susceptible individuals in terms of inflammatory cells infiltration, and tissue dissociation of mucosal layer. 16S rRNA sequencing was performed to characterize the changes in intestinal microbial community, in which Vibrio increased but Stenotrophomonas, Chryseobacterium, Delftia, and Salinivibrio decreased in the susceptible group. RNA-seq analysis indicated that 1,986 differentially expressed genes (DEGs) were detected in the susceptible group, significantly more than 310 in the resistant group, when compared to the control group. DEGs in susceptible group were significantly enriched in immune-related GO terms, such as antigen processing and presentation, MHC protein complex, and immune response, and pathways, including antigen processing and presentation, phagosome, and proteasome. Through an integrative analysis of different intestinal microbes and host DEGs, 207 strong gene-microbial correlations were identified. These findings indicate that V. harveyi infection severely damages the intestinal tissue, substantially alters the composition of intestinal microbiome and the expression of host genes, especially in susceptible individuals, and the intestinal microbiome may interact with host genes to regulate the vibriosis resistance in Chinese tongue sole.