Identification of lichen samples suspect as the cause of shrimp disease in aquaculture ponds in Vietnam by shotgun metagenomic analysis

Shrimp farming is a popular occupation in coastal provinces of Vietnam, contributing an important part to the income of people in these areas as well as creating a large output for export to foreign countries. Farmed shrimp are likely to face many risks due to disease and the stunted growth. For easy solving those problems shrimp farmers may use a lot of antibiotics, leading to antibiotic residues accumulating in the shrimp and creating antibiotic resistance in the surrounding organisms and environment. The report focuses on analyzing of a potential reason that affected the yield of shrimp farming, in which a fast-growing lichen species is suspected. Using shotgun metagenomics combined with bioinformatics analysis, this study analyzed microbial compositions of lichen samples collected from shrimp farms in the Northern and Southern region of Vietnam with a symptom of stunted growth (M01 and NM1E2, respectively). The results showed that NM1E2 had a significant high amount of potential pathogenic bacteria, including Vibrio , Shewanella , and Tenacibaculum , which could associate with biofilm formation and disease outbreaks in shrimp; the fungal sequence analysis revealed the higher abundance of opportunistic and toxin-producing genera such as Botrytis , Candida , and Fusarium in NM1E2, while M01 hosted cyanobacteria and decomposer bacteria which indicating a relatively more stable but organic-rich environment; The presence of Encephalitozoon (Microsporidia) in both samples suggests a persistent risk of latent infection; and finally, NM1E2 may act as reservoirs for pathogenic microorganisms, highlighting the importance of controlling biofilm growth and regularly monitoring microbial communities. Targeted environmental management and improved biosecurity measures are recommended to mitigate disease risks and enhance shrimp farm sustainability.