{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T23:30:09Z","timestamp":1790033409665,"version":"4.0.1"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T00:00:00Z","timestamp":1786060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"The National Key R&D Program of China","award":["2024YFD2401102"],"award-info":[{"award-number":["2024YFD2401102"]}]},{"name":"The Project supported by Southern Marine Science and Engineering Guangdong Laboratory","award":["SML2024SP003"],"award-info":[{"award-number":["SML2024SP003"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["24xkjc024"],"award-info":[{"award-number":["24xkjc024"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the 2025 Guangdong Provincial Dedicated Funds for State Key Laboratories"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Adv. Biotechnol."],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Traditional pathogen isolation can establish disease causality but often fails in complex infections involving unknown or multiple microbial backgrounds, whereas metatranscriptomics comprehensively captures the total infectome without directly resolving the primary etiological agent. Here, using overwintering syndrome (OWS) in grass carp, a widespread but unresolved aquaculture disease in China, as a disease model, we developed an integrated strategy that links comparative total infectome analysis with targeted isolation, experimental infection, and post-challenge infectome validation. Multi-organ metatranscriptomic profiling of healthy and diseased grass carp identified 107 microorganisms spanning viruses, bacteria, and eukaryotic microbes. Comparative infectomics prioritized\n                    <jats:italic>Flavobacterium psychrophilum<\/jats:italic>\n                    through its consistent disease enrichment, lesion-site abundance, multi-organ dissemination, and recurrence across affected hosts. Infection with\n                    <jats:italic>F. psychrophilum<\/jats:italic>\n                    alone reproduced the clinical signs, tissue pathology, mortality patterns, and infectome signatures of natural OWS, establishing it as the primary etiological agent. Temperature-shift experiments further showed that disease progression is promoted by warming from low temperature conditions, explaining the seasonal emergence of OWS. This work resolves a major grass carp disease and provides a generalizable framework for converting unbiased pathogen discovery into causal inference in complex infectious disease systems.\n                  <\/jats:p>","DOI":"10.1007\/s44307-026-00125-8","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T04:07:33Z","timestamp":1786075653000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A total infectome framework for resolving complex disease etiology in aquaculture"],"prefix":"10.1007","volume":"4","author":[{"given":"Yichun","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanlin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weichen","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuchao","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naiyou","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cancan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renjun","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Defeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaoping","family":"Weng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mang","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianguo","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,7]]},"reference":[{"key":"125_CR1","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1007\/s10499-022-00983-8","volume":"31","author":"M Abdelsalam","year":"2023","unstructured":"Abdelsalam M, Elgendy MY, Elfadadny MR, Ali SS, Sherif AH, Abolghait SK. A review of molecular diagnoses of bacterial fish diseases. Aquacult Int. 2023;31:417\u201334. https:\/\/doi.org\/10.1007\/s10499-022-00983-8.","journal-title":"Aquacult Int"},{"key":"125_CR2","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.applanim.2006.09.001","volume":"104","author":"PJ Ashley","year":"2007","unstructured":"Ashley PJ. Fish welfare: current issues in aquaculture. Appl Anim Behav Sci. 2007;104:199\u2013235. https:\/\/doi.org\/10.1016\/j.applanim.2006.09.001.","journal-title":"Appl Anim Behav Sci"},{"key":"125_CR3","doi-asserted-by":"publisher","first-page":"40","DOI":"10.2174\/1874401X01104010040","volume":"4","author":"ME Barnes","year":"2011","unstructured":"Barnes ME, Brown ML. A review of Flavobacterium psychrophilum biology, clinical signs, and bacterial cold water disease prevention and treatment. Open Fish Sci J. 2011;4:40\u20138.","journal-title":"Open Fish Sci J"},{"key":"125_CR4","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1016\/j.autrev.2012.12.005","volume":"12","author":"DP Bogdanos","year":"2013","unstructured":"Bogdanos DP, Smyk DS, Invernizzi P, Rigopoulou EI, Blank M, Pouria S, et al. Infectome: a platform to trace infectious triggers of autoimmunity. Autoimmun Rev. 2013;12:726\u201340. https:\/\/doi.org\/10.1016\/j.autrev.2012.12.005.","journal-title":"Autoimmun Rev"},{"key":"125_CR5","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1007\/s10482-013-9980-7","volume":"104","author":"J Bondoso","year":"2013","unstructured":"Bondoso J, Harder J, Lage OM. rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales. Antonie Van Leeuwenhoek. 2013;104:477\u201388. https:\/\/doi.org\/10.1007\/s10482-013-9980-7.","journal-title":"Antonie Van Leeuwenhoek"},{"key":"125_CR6","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59\u201360. https:\/\/doi.org\/10.1038\/nmeth.3176.","journal-title":"Nat Methods"},{"key":"125_CR7","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2023.1109461","volume":"14","author":"LF Canosa","year":"2023","unstructured":"Canosa LF, Bertucci JI. The effect of environmental stressors on growth in fish and its endocrine control. Front Endocrinol (Lausanne). 2023;14:1109461. https:\/\/doi.org\/10.3389\/fendo.2023.1109461.","journal-title":"Front Endocrinol (Lausanne)"},{"key":"125_CR8","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","unstructured":"Capella-Guti\u00e9rrez S, Silla-Mart\u00ednez JM, Gabald\u00f3n T. TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btp348.","journal-title":"Bioinformatics"},{"key":"125_CR9","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","volume":"20","author":"CY Chiu","year":"2019","unstructured":"Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019;20:341\u201355. https:\/\/doi.org\/10.1038\/s41576-019-0113-7.","journal-title":"Nat Rev Genet"},{"key":"125_CR10","doi-asserted-by":"publisher","DOI":"10.1016\/j.micpath.2023.106400","volume":"185","author":"M Dayana Senthamarai","year":"2023","unstructured":"Dayana Senthamarai M, Rajan MR, Bharathi PV. Current risks of microbial infections in fish and their prevention methods: a review. Microb Pathog. 2023;185:106400. https:\/\/doi.org\/10.1016\/j.micpath.2023.106400.","journal-title":"Microb Pathog"},{"key":"125_CR11","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.965099","volume":"13","author":"F Deng","year":"2022","unstructured":"Deng F, Wang D, Loch TP, Chen F, Lu T, Cao Y, et al. Time-course transcriptome analyses of spleen in rainbow trout (Oncorhynchus mykiss) post-Flavobacterium psychrophilum infection. Front Immunol. 2022;13:965099. https:\/\/doi.org\/10.3389\/fimmu.2022.965099.","journal-title":"Front Immunol"},{"key":"125_CR12","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsi.2023.109305","volume":"144","author":"F Deng","year":"2024","unstructured":"Deng F, Wang D, Yu Y, Lu T, Li S. Systemic immune response of rainbow trout exposed to Flavobacterium psychrophilum infection. Fish Shellfish Immunol. 2024;144:109305. https:\/\/doi.org\/10.1016\/j.fsi.2023.109305.","journal-title":"Fish Shellfish Immunol"},{"key":"125_CR13","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1685035","author":"G Destras","year":"2026","unstructured":"Destras G, Sabatier M, Bal A, Simon B, Semanas Q, Regue H, et al. Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response. Front Microbiol. 2026. https:\/\/doi.org\/10.3389\/fmicb.2025.1685035.","journal-title":"Front Microbiol"},{"key":"125_CR14","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s13073-025-01447-3","volume":"17","author":"AC Doxey","year":"2025","unstructured":"Doxey AC, Abu Mazen N, Homm M, Chu V, Hunjan M, Lobb B, et al. Metatranscriptomic profiling reveals pathogen and host response signatures of pediatric acute sinusitis and upper respiratory infection. Genome Med. 2025;17:22. https:\/\/doi.org\/10.1186\/s13073-025-01447-3.","journal-title":"Genome Med"},{"key":"125_CR15","doi-asserted-by":"publisher","unstructured":"FAO. The state of world fisheries and aquaculture 2024 - blue transformation in action. Italy: Rome. 2024. https:\/\/doi.org\/10.4060\/cd0683en.","DOI":"10.4060\/cd0683en"},{"key":"125_CR16","doi-asserted-by":"publisher","DOI":"10.3390\/cells15020157","volume":"15","author":"Y Feng","year":"2026","unstructured":"Feng Y, Geng Y, Liu S, Huang X, Mou C, Zhao H, et al. Overwinter syndrome in grass carp (Ctenopharyngodon idellus) links enteric viral proliferation to mucosal disruption via multiomics investigation. Cells. 2026a;15:157. https:\/\/doi.org\/10.3390\/cells15020157.","journal-title":"Cells"},{"key":"125_CR17","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsi.2025.110965","volume":"168","author":"Y Feng","year":"2026","unstructured":"Feng Y, Liu S, Huang X, Geng Y, Mou C, Zhao H, et al. Ferroptosis triggered by gill dysbiosis mediates immune failure in grass carp overwintering syndrome. Fish Shellfish Immunol. 2026b;168:110965. https:\/\/doi.org\/10.1016\/j.fsi.2025.110965.","journal-title":"Fish Shellfish Immunol"},{"key":"125_CR18","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1128\/CMR.9.1.18","volume":"9","author":"DN Fredricks","year":"1996","unstructured":"Fredricks DN, Relman DA. Sequence-based identification of microbial pathogens: a reconsideration of Koch\u2019s postulates. Clin Microbiol Rev. 1996;9:18\u201333. https:\/\/doi.org\/10.1128\/CMR.9.1.18.","journal-title":"Clin Microbiol Rev"},{"key":"125_CR19","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","volume":"28","author":"L Fu","year":"2012","unstructured":"Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/bts565.","journal-title":"Bioinformatics"},{"key":"125_CR20","doi-asserted-by":"publisher","first-page":"1593","DOI":"10.1128\/AEM.01717-10","volume":"77","author":"S Hesami","year":"2011","unstructured":"Hesami S, Metcalf DS, Lumsden JS, MacInnes JI. Identification of cold-temperature-regulated genes in Flavobacterium psychrophilum. Appl Environ Microbiol. 2011;77:1593\u2013600. https:\/\/doi.org\/10.1128\/AEM.01717-10.","journal-title":"Appl Environ Microbiol"},{"key":"125_CR21","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-023-01570-6","volume":"11","author":"D Hou","year":"2023","unstructured":"Hou D, Lian T, Guo G, Gong H, Wu C, Han P, et al. Integration of microbiome and Koch\u2019s postulates to reveal multiple bacterial pathogens of whitish muscle syndrome in mud crab, Scylla paramamosain. Microbiome. 2023;11:155. https:\/\/doi.org\/10.1186\/s40168-023-01570-6.","journal-title":"Microbiome"},{"key":"125_CR22","doi-asserted-by":"publisher","first-page":"122","DOI":"10.3201\/eid0802.010141","volume":"8","author":"P Houpikian","year":"2002","unstructured":"Houpikian P, Raoult D. Traditional and molecular techniques for the study of emerging bacterial diseases: one laboratory\u2019s perspective. Emerg Infect Dis. 2002;8:122\u201331. https:\/\/doi.org\/10.3201\/eid0802.010141.","journal-title":"Emerg Infect Dis"},{"key":"125_CR23","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquaculture.2019.734811","volume":"517","author":"X Huang","year":"2020","unstructured":"Huang X, Xiong G, Feng Y, Wang K, Liu Y, Zhong L, et al. Ulcerative disease emergence in grass carp (Ctenopharyngodon idellus) aquaculture in China: possible impact of temperature abnormality. Aquaculture. 2020;517:734811. https:\/\/doi.org\/10.1016\/j.aquaculture.2019.734811.","journal-title":"Aquaculture"},{"key":"125_CR24","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/s40168-022-01265-4","volume":"10","author":"X Huang","year":"2022","unstructured":"Huang X, Wu W, Tian X, Hou X, Cui X, Xiao Y, et al. A total infectome approach to understand the etiology of infectious disease in pigs. Microbiome. 2022;10:73. https:\/\/doi.org\/10.1186\/s40168-022-01265-4.","journal-title":"Microbiome"},{"key":"125_CR25","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1016\/j.tim.2023.01.012","volume":"31","author":"KS Hutson","year":"2023","unstructured":"Hutson KS, Davidson IC, Bennett J, Poulin R, Cahill PL. Assigning cause for emerging diseases of aquatic organisms. Trends Microbiol. 2023;31:681\u201391. https:\/\/doi.org\/10.1016\/j.tim.2023.01.012.","journal-title":"Trends Microbiol"},{"key":"125_CR26","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","volume":"30","author":"K Katoh","year":"2002","unstructured":"Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: A novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 2002;30:3059\u201366. https:\/\/doi.org\/10.1093\/nar\/gkf436.","journal-title":"Nucleic Acids Res"},{"key":"125_CR27","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/S0044-8486(00)00424-5","volume":"191","author":"N Kautsky","year":"2000","unstructured":"Kautsky N, R\u00f6nnb\u00e4ck P, Tedengren M, Troell M. Ecosystem perspectives on management of disease in shrimp pond farming. Aquaculture. 2000;191:145\u201361. https:\/\/doi.org\/10.1016\/S0044-8486(00)00424-5.","journal-title":"Aquaculture"},{"key":"125_CR28","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1186\/s13567-016-0383-4","volume":"47","author":"MH Kotob","year":"2016","unstructured":"Kotob MH, Menanteau-Ledouble S, Kumar G, Abdelzaher M, El-Matbouli M. The impact of co-infections on fish: a review. Vet Res. 2016;47:98. https:\/\/doi.org\/10.1186\/s13567-016-0383-4.","journal-title":"Vet Res"},{"key":"125_CR29","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msae263","volume":"41","author":"S Kumar","year":"2024","unstructured":"Kumar S, Stecher G, Suleski M, Sanderford M, Sharma S, Tamura K. MEGA12: molecular evolutionary genetic analysis version 12 for adaptive and green computing. Mol Biol Evol. 2024;41:msae263. https:\/\/doi.org\/10.1093\/molbev\/msae263.","journal-title":"Mol Biol Evol"},{"key":"125_CR30","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357\u20139. https:\/\/doi.org\/10.1038\/nmeth.1923.","journal-title":"Nat Methods"},{"key":"125_CR31","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25:2078\u20139. https:\/\/doi.org\/10.1093\/bioinformatics\/btp352.","journal-title":"Bioinformatics"},{"key":"125_CR32","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","volume":"31","author":"D Li","year":"2015","unstructured":"Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de bruijn graph. Bioinformatics. 2015;31:1674\u20136. https:\/\/doi.org\/10.1093\/bioinformatics\/btv033.","journal-title":"Bioinformatics"},{"key":"125_CR33","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s40168-019-0618-5","volume":"7","author":"F Li","year":"2019","unstructured":"Li F, Hitch TCA, Chen Y, Creevey CJ, Guan LL. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. Microbiome. 2019;7:6. https:\/\/doi.org\/10.1186\/s40168-019-0618-5.","journal-title":"Microbiome"},{"key":"125_CR34","doi-asserted-by":"publisher","DOI":"10.1016\/j.aqrep.2022.101267","volume":"25","author":"H Liang","year":"2022","unstructured":"Liang H, Xu H, Ge X, Zhu J, Ren M, Mi H. Water temperature affects the protein requirements, growth performance, and nutritional metabolism of grass carp (Ctenopharyngodon idella) juveniles. Aquac Rep. 2022;25:101267. https:\/\/doi.org\/10.1016\/j.aqrep.2022.101267.","journal-title":"Aquac Rep"},{"key":"125_CR35","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/nrmicro2949","volume":"11","author":"WI Lipkin","year":"2013","unstructured":"Lipkin WI. The changing face of pathogen discovery and surveillance. Nat Rev Microbiol. 2013;11:133\u201341. https:\/\/doi.org\/10.1038\/nrmicro2949.","journal-title":"Nat Rev Microbiol"},{"key":"125_CR36","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquaculture.2025.742606","volume":"607","author":"H Ma","year":"2025","unstructured":"Ma H, Wang G, Huang T, Liu E, Gu W, Xu G. Whole-genome resequencing reveals selection signatures in China\u2019s first rainbow trout (Oncorhynchus mykiss) strain \u201cShuike no. 1.\u201d Aquaculture. 2025;607:742606. https:\/\/doi.org\/10.1016\/j.aquaculture.2025.742606.","journal-title":"Aquaculture"},{"key":"125_CR37","doi-asserted-by":"publisher","first-page":"169","DOI":"10.3354\/dao036169","volume":"36","author":"L Madsen","year":"1999","unstructured":"Madsen L, Dalsgaard I. Reproducible methods for experimental infection with Flavobacterium psychrophilum in rainbow trout Oncorhynchus mykiss. Dis Aquat Organ. 1999;36:169\u201376. https:\/\/doi.org\/10.3354\/dao036169.","journal-title":"Dis Aquat Organ"},{"key":"125_CR38","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/S0923-2508(99)80061-8","volume":"150","author":"C Michel","year":"1999","unstructured":"Michel C, Antonio D, Hedrick RP. Production of viable cultures of Flavobacterium psychrophilum: approach and control. Res Microbiol. 1999;150:351\u20138. https:\/\/doi.org\/10.1016\/S0923-2508(99)80061-8.","journal-title":"Res Microbiol"},{"key":"125_CR39","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/nature02759","volume":"430","author":"DM Morens","year":"2004","unstructured":"Morens DM, Folkers GK, Fauci AS. The challenge of emerging and re-emerging infectious diseases. Nature. 2004;430:242\u20139. https:\/\/doi.org\/10.1038\/nature02759.","journal-title":"Nature"},{"key":"125_CR40","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1186\/s13104-024-06951-0","volume":"17","author":"G Nabakooza","year":"2024","unstructured":"Nabakooza G, Wagner DD, Momin N, Marine RL, Weldon WC, Oberste MS. Sequence-matching adapter trimmers generate consistent quality and assembly metrics for illumina sequencing of RNA viruses. BMC Res Notes. 2024;17:308. https:\/\/doi.org\/10.1186\/s13104-024-06951-0.","journal-title":"BMC Res Notes"},{"key":"125_CR41","doi-asserted-by":"crossref","unstructured":"Nematollahi A, Decostere A, Pasmans F, Haesebrouck F. Flavobacterium psychrophilum infections in salmonid fish. 2003.","DOI":"10.1046\/j.1365-2761.2003.00488.x"},{"key":"125_CR42","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","volume":"32","author":"L-T Nguyen","year":"2015","unstructured":"Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268\u201374. https:\/\/doi.org\/10.1093\/molbev\/msu300.","journal-title":"Mol Biol Evol"},{"key":"125_CR43","doi-asserted-by":"publisher","first-page":"266","DOI":"10.3390\/parasitologia2040023","volume":"2","author":"E O\u2019Halloran","year":"2022","unstructured":"O\u2019Halloran E, Mooney R, Rodgers K, Henriquez FL. Microbial interactions that contribute to gill disease in aquaculture. Parasitologia (Rome). 2022;2:266\u201391. https:\/\/doi.org\/10.3390\/parasitologia2040023.","journal-title":"Parasitologia (Rome)"},{"key":"125_CR44","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1111\/raq.12192","volume":"10","author":"B Oidtmann","year":"2018","unstructured":"Oidtmann B, Dixon P, Way K, Joiner C, Bayley AE. Risk of waterborne virus spread \u2013 review of survival of relevant fish and crustacean viruses in the aquatic environment and implications for control measures. Rev Aquac. 2018;10:641\u201369. https:\/\/doi.org\/10.1111\/raq.12192.","journal-title":"Rev Aquac"},{"key":"125_CR45","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1016\/j.molmed.2023.02.002","volume":"29","author":"T Ojala","year":"2023","unstructured":"Ojala T, Kankuri E, Kankainen M. Understanding human health through metatranscriptomics. Trends Mol Med. 2023;29:376\u201389. https:\/\/doi.org\/10.1016\/j.molmed.2023.02.002.","journal-title":"Trends Mol Med"},{"key":"125_CR46","doi-asserted-by":"publisher","DOI":"10.1016\/j.fsirep.2023.100096","volume":"4","author":"EM Okon","year":"2023","unstructured":"Okon EM, Okocha RC, Taiwo AB, Michael FB, Bolanle AM. Dynamics of co-infection in fish: a review of pathogen-host interaction and clinical outcome. Fish Shellfish Immunol Rep. 2023;4:100096. https:\/\/doi.org\/10.1016\/j.fsirep.2023.100096.","journal-title":"Fish Shellfish Immunol Rep"},{"key":"125_CR47","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590\u20136. https:\/\/doi.org\/10.1093\/nar\/gks1219.","journal-title":"Nucleic Acids Res"},{"key":"125_CR48","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquaculture.2023.740047","volume":"578","author":"P Rameshkumar","year":"2024","unstructured":"Rameshkumar P, Balachandran C, Vairamuthu S, Dhinakar Raj G, John Kirubaharan J, Nagarajan K, et al. Co-infection of viral nervous necrosis (VNN) and bacterial infection outbreak in cage cultured cobia fingerlings. Aquaculture. 2024;578:740047. https:\/\/doi.org\/10.1016\/j.aquaculture.2023.740047.","journal-title":"Aquaculture"},{"key":"125_CR49","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1111\/j.1471-8286.2007.01678.x","volume":"7","author":"S Ratnasingham","year":"2007","unstructured":"Ratnasingham S, Hebert PDN. Bold: the barcode of life data system (http:\/\/www.barcodinglife.org). Mol Ecol Notes. 2007;7:355\u201364. https:\/\/doi.org\/10.1111\/j.1471-8286.2007.01678.x.","journal-title":"Mol Ecol Notes"},{"key":"125_CR50","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/s42523-024-00344-1","volume":"6","author":"G Raymo","year":"2024","unstructured":"Raymo G, Januario F, Ali A, Ahmed RO, Al-Tobasei R, Salem M. Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout. Anim Microbiome. 2024;6:57. https:\/\/doi.org\/10.1186\/s42523-024-00344-1.","journal-title":"Anim Microbiome"},{"key":"125_CR51","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1093\/oxfordjournals.molbev.a026104","volume":"16","author":"AJ Roger","year":"1999","unstructured":"Roger AJ, Sandblom O, Doolittle WF, Philippe H. An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes. Mol Biol Evol. 1999;16:218\u201333. https:\/\/doi.org\/10.1093\/oxfordjournals.molbev.a026104.","journal-title":"Mol Biol Evol"},{"key":"125_CR52","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-03458-6","volume":"7","author":"AJ Sabat","year":"2017","unstructured":"Sabat AJ, van Zanten E, Akkerboom V, Wisselink G, van Slochteren K, de Boer RF, et al. Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species. Sci Rep. 2017;7:3434. https:\/\/doi.org\/10.1038\/s41598-017-03458-6.","journal-title":"Sci Rep"},{"key":"125_CR53","doi-asserted-by":"publisher","first-page":"890","DOI":"10.5455\/javar.2025.l951","volume":"12","author":"ME Shafi","year":"2025","unstructured":"Shafi ME. A comprehensive review of summer mortality syndrome in fish: causes, climate impact, and mitigation strategies. J Adv Vet Anim Res. 2025;12:890\u2013907. https:\/\/doi.org\/10.5455\/javar.2025.l951.","journal-title":"J Adv Vet Anim Res"},{"key":"125_CR54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010259","volume":"18","author":"M Shi","year":"2022","unstructured":"Shi M, Zhao S, Yu B, Wu W-C, Hu Y, Tian J-H, et al. Total infectome characterization of respiratory infections in pre-COVID-19 wuhan. China PLOS Pathogens. 2022;18:e1010259. https:\/\/doi.org\/10.1371\/journal.ppat.1010259.","journal-title":"China PLOS Pathogens"},{"key":"125_CR55","doi-asserted-by":"publisher","first-page":"5593","DOI":"10.3390\/su17125593","volume":"17","author":"Y Song","year":"2025","unstructured":"Song Y, Zhang W. Balancing growth and sustainability in China\u2019s carp aquaculture: practices, policies, and sustainability pathways. Sustainability. 2025;17:5593. https:\/\/doi.org\/10.3390\/su17125593.","journal-title":"Sustainability"},{"key":"125_CR56","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.jare.2010.04.001","volume":"2","author":"CE Starliper","year":"2011","unstructured":"Starliper CE. Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum. J Adv Res. 2011;2:97\u2013108. https:\/\/doi.org\/10.1016\/j.jare.2010.04.001.","journal-title":"J Adv Res"},{"key":"125_CR57","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00636-24","volume":"9","author":"Y Sun","year":"2024","unstructured":"Sun Y, Xing J, Xu S, Li Y, Zhong J, Gao H, et al. Demographic and zoological drivers of infectome diversity in companion cats with ascites. mSystems. 2024;9:e00636-24. https:\/\/doi.org\/10.1128\/msystems.00636-24.","journal-title":"mSystems"},{"key":"125_CR58","doi-asserted-by":"publisher","DOI":"10.3390\/fishes9050163","volume":"9","author":"V Vaibarov\u00e1","year":"2024","unstructured":"Vaibarov\u00e1 V, \u010c\u00ed\u017eek A. Supposed virulence factors of Flavobacterium psychrophilum: a review. Fishes. 2024;9:163. https:\/\/doi.org\/10.3390\/fishes9050163.","journal-title":"Fishes"},{"key":"125_CR59","doi-asserted-by":"publisher","DOI":"10.3390\/v10020076","volume":"10","author":"S Venkataraman","year":"2018","unstructured":"Venkataraman S, Prasad BVLS, Selvarajan R. RNA dependent RNA polymerases: insights from structure, function and evolution. Viruses. 2018;10:76. https:\/\/doi.org\/10.3390\/v10020076.","journal-title":"Viruses"},{"key":"125_CR60","doi-asserted-by":"publisher","DOI":"10.3390\/v16010062","volume":"16","author":"R Wang","year":"2023","unstructured":"Wang R, Liu S, Sun H, Xu C, Wen Y, Wu X, et al. Metatranscriptomics reveals the RNA virome of Ixodes persulcatus in the China\u2013North Korea border, 2017. Viruses. 2023;16:62. https:\/\/doi.org\/10.3390\/v16010062.","journal-title":"Viruses"},{"key":"125_CR61","doi-asserted-by":"publisher","first-page":"2327","DOI":"10.1056\/NEJMoa1803396","volume":"380","author":"MR Wilson","year":"2019","unstructured":"Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, et al. Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis. N Engl J Med. 2019;380:2327\u201340. https:\/\/doi.org\/10.1056\/NEJMoa1803396.","journal-title":"N Engl J Med"},{"key":"125_CR62","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquaculture.2025.743170","volume":"612","author":"Y Xiao","year":"2026","unstructured":"Xiao Y, Zhao Z, Pan Y, Gao S, Zhao D, Dong Y, et al. Seawater adaptation of freshwater cultured rainbow trout (Oncorhynchus mykiss): insights into the gut microbiota and tissue gene expression profiles. Aquaculture. 2026;612:743170. https:\/\/doi.org\/10.1016\/j.aquaculture.2025.743170.","journal-title":"Aquaculture"},{"key":"125_CR63","doi-asserted-by":"publisher","first-page":"11299","DOI":"10.1038\/s41467-025-66462-9","volume":"16","author":"G Xin","year":"2025","unstructured":"Xin G, Wang D, Zhang X, Cen Q, Peng M, Liao Y, et al. Infectome analysis of small mammals in southern China reveals pathogen ecology and emerging risks. Nat Commun. 2025;16:11299. https:\/\/doi.org\/10.1038\/s41467-025-66462-9.","journal-title":"Nat Commun"},{"key":"125_CR64","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/S1473-3099(04)01044-8","volume":"4","author":"S Yang","year":"2004","unstructured":"Yang S, Rothman RE. PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect Dis. 2004;4:337\u201348. https:\/\/doi.org\/10.1016\/S1473-3099(04)01044-8.","journal-title":"Lancet Infect Dis"},{"key":"125_CR65","doi-asserted-by":"publisher","first-page":"1613","DOI":"10.1099\/ijsem.0.001755","volume":"67","author":"S-H Yoon","year":"2017","unstructured":"Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613\u20137. https:\/\/doi.org\/10.1099\/ijsem.0.001755.","journal-title":"Int J Syst Evol Microbiol"}],"container-title":["Advanced Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s44307-026-00125-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s44307-026-00125-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s44307-026-00125-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T04:07:35Z","timestamp":1786075655000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s44307-026-00125-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,7]]},"references-count":65,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["125"],"URL":"https:\/\/doi.org\/10.1007\/s44307-026-00125-8","relation":{},"ISSN":["2948-2801"],"issn-type":[{"value":"2948-2801","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,7]]},"assertion":[{"value":"24 June 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2026","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 July 2026","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 August 2026","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Author J.G.H. is an Editorial Board member of Advanced Biotechnology, and was not involved in the peer review and editorial decisions for this manuscript.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"31"}}