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

Identification of lichen samples suspect as the cause of shrimp disease in aquaculture ponds in Vietnam by shotgun metagenomic analysis | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Identification of lichen samples suspect as the cause of shrimp disease in aquaculture ponds in Vietnam by shotgun metagenomic analysis Trong Luong Vu, Thi Minh Huyen Nguyen, Phu Hiep Hoang, Thuy Linh Phung, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6886889/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract 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. Shrimp farming lichen fungal identification microbial community metagenomic analysis Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6886889","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":472418217,"identity":"cbb1f826-2b43-4eee-ac03-8b03a547615d","order_by":0,"name":"Trong Luong Vu","email":"","orcid":"","institution":"Thai Nguyen University of Education","correspondingAuthor":false,"prefix":"","firstName":"Trong","middleName":"Luong","lastName":"Vu","suffix":""},{"id":472418218,"identity":"c43d9406-7903-4dfa-9c4e-4c84ebd056be","order_by":1,"name":"Thi Minh Huyen 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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 \u003cem\u003eVibrio\u003c/em\u003e, \u003cem\u003eShewanella\u003c/em\u003e, and \u003cem\u003eTenacibaculum\u003c/em\u003e, 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 \u003cem\u003eBotrytis\u003c/em\u003e, \u003cem\u003eCandida\u003c/em\u003e, and \u003cem\u003eFusarium\u003c/em\u003e in NM1E2, while M01 hosted cyanobacteria and decomposer bacteria which indicating a relatively more stable but organic-rich environment; The presence of \u003cem\u003eEncephalitozoon\u003c/em\u003e (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.\u003c/p\u003e","manuscriptTitle":"Identification of lichen samples suspect as the cause of shrimp disease in aquaculture ponds in Vietnam by shotgun metagenomic analysis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-18 15:21:00","doi":"10.21203/rs.3.rs-6886889/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"8c670f14-9bf6-41dd-8992-b8ba3f842c0b","owner":[],"postedDate":"June 18th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-07-05T18:53:12+00:00","versionOfRecord":[],"versionCreatedAt":"2025-06-18 15:21:00","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6886889","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6886889","identity":"rs-6886889","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}