Dysbiosis of the shrimp ( Penaeus monodon ) gut microbiome with AHPND outbreaks revealed by 16S rRNA metagenomics analysis

Abstract

Acute hepatopancreatic necrosis disease (AHPND) or early mortality syndrome (EMS) is a severe hepatopancreatic disease of shrimp, caused mainly by Vibrio parahaemolyticus. Growing evidence has shown that gut bacterial imbalance is linked to bacterial pathogenesis. AHPND disease also imposes selective pressure on the gut microbiota, which was revealed by metagenomic analysis of 16S rRNA gene. Firstly, 46 bacterial strains and 8 V. parahaemolyticus were isolated from the intestine of AHPND-infected Penaeus monodon. Secondly, PCR detection of 4 major virulence genes was carried out in 8 V. parahaemolyticus. The results showed that pirAVp could be detected in 5 strains. Thirdly, 16S rRNA gene was used to sequence the intestinal microbiota of asymptomatic and AHPND-infected shrimp. There were significant differences in gut bacteria structure between the two groups, because pirAVp toxin alone is sufficient to change the core microbiota of infected shrimp. The microbial communities of infected shrimp were enriched with Firmicutes and Bacteroidetes, but the number of Proteobacteria was reduced compared with the healthy shrimps. However, in healthy shrimp, the core microbial abundance was opposite to that of infected shrimp. AHPND infection was positively correlated with the levels of SCFAs (butyrate and propionate) producing species such as Bacteroides, Bifidobacterium, Lactobacillus and Staphylococcus. Significant differences were found in the functional gene profile category between healthy and infected shrimp gut. These findings improve the current understanding of AHPND disease's impact on the assembly of shrimp gut microbiota.