Response signatures of Litopenaeus vannamei to natural Enterocytozoon hepatopenaei infection revealed by the integration of the microbiome and transcriptome

Enterocytozoon hepatopenaei (EHP) is a parasite that causes hepatopancreatic microsporidiosis and is associated with shrimp growth retardation. The intestinal bacterial is an important biological barrier against pathogen invasion. In this study, we investigated the intestinal bacterial and hepatopancreas transcriptome responses of Litopenaeus vannamei to natural EHP infection. Compared with the healthy group, obvious changes in the intestinal bacterial were caused by EHP infection, with significantly increased relative abundance of Chloroflexi and decreased relative abundance of Bacteroidetes. Several genera of bacteria with putatively beneficial substance-producing characteristics were reduced in the diseased group, such as Alloprevotella, Bacillus, Bacteroides, Weissella, and Pandoraea. The hepatopancreas transcriptome revealed differentially expressed genes mainly associated with carbohydrate digestion and absorption, and some immune-related genes associated with antimicrobial processes were downregulated in contrasting accessions. Bacillus had the mostly positive correlation with gene markers; Tryp and Fer2 had positive correlation with intestinal bacteria, but APOD, FABP and HSP67 had negative correlation with them. These results revealed that EHP infection causes intestinal bacterial variation and influences the nutrition metabolism and immunity of L. vannamei.