Characterization of Microbiome Diversity in the Digestive Tract of Penaeus vannamei Fed with Probiotics and Challenged with Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease

The microbiome of the shrimp's digestive tract shows differences between healthy and acute hepatopancreatic necrosis disease (AHPND)-affected shrimp. The present study aimed to evaluate the impact of probiotic consumption on the microbial community in experimentally AHPND-infected shrimp. Effective probiotics (EPs) <i>Vibrio alginolyticus</i> (Va32A), <i>V. campbellii</i> (VcHA), and <i>Bacillus pumilus</i> (BPY100) and non-effective probiotics (NEPs) <i>B. pumilus</i> (Bp43, and BpY119), were employed in bioassays with <i>Penaeus vannamei</i> and challenged with AHPND-causing <i>V. parahaemolyticus</i> (Vp_AHPND). Stomach (Sto), intestine (Int), and hepatopancreas (Hep) were analyzed by metabarcoding (16S rRNA gene) to characterize the microbiome and biomarkers. Hep-VcHA showed the highest alpha diversity (Shannon index = 5.88; 166 ASVs), whereas the lowest was for Hep-Bp43 (2.33; 7 ASVs). Proteobacteria, Actinobacteria, Bacteroidetes, and Saccharibacteria were the most abundant phyla. The relative abundance of <i>Vibrio</i> sp. was the highest in the Hep and Int of Bp43, BPY119 and the positive control, followed by <i>Rhodobacteraceae</i> in the EP group. Principle coordinate analysis (PCoA) showed a cluster grouped negative (Sto and Hep) control with almost all organs in the EP group causing 28.79% of the variation. The core microbiome of EP was mainly represented by <i>Rhodobacteraceae</i>, Caldilineaceae, <i>Celeribacter indicus</i>, <i>Illumatobacter</i>, <i>Microbacterium</i>, <i>Ruegeria atlantica, Saccharibacteria</i> sp., <i>Shimia biformata</i>, and <i>Thalassobius mediterraneus</i>, whose relative abundance was enriched by probiotics, which may explain their protective roles against Vp_AHPND, whereas the low survival in the NEP group was associated with a higher diversity of <i>Vibrio</i> spp. Our results present an ecosystem-friendly alternative based on beneficial microorganisms to prevent and control AHPND and probably other bacterial diseases in shrimp farming.