Integrated metabolome-SNP-gut microbiome analysis deciphers the molecular basis of EHP resistance in Penaeus vannamei
Abstract
Enterocytozoon hepatopenaei (EHP) has emerged as a highly virulent pathogen in shrimp aquaculture, yet the molecular determinants governing host resistance remain incompletely characterized. This study employed an integrated multi-omics strategy (metabolome, transcriptome, and microbiome) to elucidate the molecular basis of EHP resistance in Penaeus vannamei. Comparative metabolomic profiling of EHP-resistant (R4029) and susceptible (S4104) family lines identified 1,614 metabolites, primarily organic acids (35.07%) and lipids (21.56%). Orthogonal partial least squares discriminant analysis (OPLS-DA) revealed significant intergroup metabolic differentiation (Q2 > 0.9), with 428 and 388 metabolites exhibiting differential abundance (variable importance in projection |VIP| > 1, false discovery rate-adjusted P C) inducing a Thr253Pro substitution (full-length MRC1 sequence) that alters protein secondary structure. Gut microbiome characterization demonstrated elevated α-diversity (P < 0.05) and enhanced community stability in resistant shrimp, with selective enrichment of putatively beneficial taxa (Photobacterium, Ralstonia). Collectively, these findings suggest that EHP resistance is mediated by coordinated transcriptional and metabolic reprogramming, functionally consequential genetic polymorphisms, and stable microbial community dynamics, thereby establishing a multi-omics framework for the selective breeding of EHP-resistant shrimp.
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