Metagenomic analysis of lichen-like samples correlated to the mortality of cultured shrimp in aquaculture ponds in Vietnam

Abstract

Farmed shrimp, especially in aquaculture ponds in mainland, faced many risks due to disease and the stunted growth in Vietnam. For easy solving those problems shrimp farmers could use a lot of antibiotics, leading to antibiotic residues accumulating in the shrimp and creating antibiotic resistance in the surrounding organisms and environment. This report focused on analyzing of a fast-growing lichen-like species collected from shrimp farms in the Northern (M01) and Southern (NM1E2) region of Vietnam with a same symptom of stunted growth, respectively. Using shotgun metagenomics and bioinformatics analysis, microorganism community of lichen-like samples were identified. The results showed that Pseudomonas, Halomonas, Aeromonas, Vibrio, Shewanella, and Moraxella were the main bacterial genera contribute to the samples and haft of them (Vibrio, Shewanella, and Moraxella) could be potential pathogenic bacteria. The fungal analysis showed that both samples were colonized with Fusarium oxysporum and Fusarium graminearum, the fungus associated with plant diseases but increasingly implicated in infectious diseases in aquatic animals. The prevalence of other opportunistic fungi such as Aspergillus fumigatus also suggested that they could play a larger role in deteriorating shrimp health than originally thought. Our results are preliminary evaluation for the potential influence of the lichen-like organism in shrimp farm. The results suggest targeted environmental management and improved biosecurity measures to mitigate disease risks and enhance shrimp farm sustainability.