Probiotic properties are highly species- or even strain- specific. Strain-specific responses of growth performance, non-specific immunity, disease resistance, and intestinal microbiota in Penaeus vannamei to two Enterococcus faecium strains supplementation were investigated in this study. Basal diet (control, CON) was supplemented with E. faecium HK and LYB at the dose of 1 × 1010 CFU / kg (HK group) and 1 × 1011 CFU / kg (LYB group), respectively. The results indicated that the HK and LYB groups exhibited significant enhancements in growth performance, non-specific immunity, and disease resistance of shrimp against Vibrio parahaemolyticus compared to the control (P < 0.05). However, the specific growth rate of shrimp in the LYB group was significantly better than that in the HK group (P < 0.05). Furthermore, the HK group showed significant increases in phenoloxidase, total nitric oxide synthase activities, lysozyme content in the serum, as well as the relative expression levels of proPO, LGBP, Imd, Relish, and eIF4E2 genes in the hepatopancreas compared to the LYB group (P < 0.05). These results suggested the strain HK exhibited better non-specific immunity efficiency while the strain LYB exerted better growth enhancement in shrimp. Dietary both of strain HK and LYB significantly altered microbial community structure (P < 0.05), and the strain HK significantly improved intestinal microbial diversity in shrimp. The relative abundance of Rubritaleaceae and Rhodobacteraceae were significantly increased, whereas those of facultative anaerobes and potential pathogens (i.e., Vibrionaceae, Flavobacteriaceae and Erysipelotrichaceae, etc.) were reduced in response to dietary supplementation of E. faecium HK and LYB. Furthermore, dietary both of strain HK and LYB could promote intestinal microbial community stability by increasing average connectivity, cooperation interactions, the number of generalists within the network. When growth performance and intestinal microbial homeostasis of shrimp are considered, E. faecium LYB might be better than the strain HK in shrimp farming.
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