Christopher Riccardi, Yuqiu Wang, Shibu Yooseph, Fengzhu Sun
{"title":"共享标记物配置文件的双向亚组可实现准确的病毒分类。","authors":"Christopher Riccardi, Yuqiu Wang, Shibu Yooseph, Fengzhu Sun","doi":"10.1186/s40168-025-02159-x","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Due to the impact of viral metagenomic sequencing, the official virus taxonomy is updated several times a year, with labels being renamed even substantially across releases. While this helps reveal newer aspects on the classification of viruses, existing bioinformatic methods for classification struggle to stay in sync with this ever-improving resource.</p><p><strong>Results: </strong>We developed a new computer program, named VIRGO, that is able to correctly predict virus families from metagenomic data with an F1 score above 0.9 using a novel viral sequence similarity metric proposed in this work. Moreover, it ensures compatibility with any version of the official taxonomy of viruses.</p><p><strong>Conclusions: </strong>Virgo is designed to easily incorporate newer releases of the official taxonomy, thus representing a valuable resource in the virology community while raising awareness to develop computational methods that evolve alongside manually curated resources. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"170"},"PeriodicalIF":12.7000,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12291348/pdf/","citationCount":"0","resultStr":"{\"title\":\"Bidirectional subsethood of shared marker profiles enables accurate virus classification.\",\"authors\":\"Christopher Riccardi, Yuqiu Wang, Shibu Yooseph, Fengzhu Sun\",\"doi\":\"10.1186/s40168-025-02159-x\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Due to the impact of viral metagenomic sequencing, the official virus taxonomy is updated several times a year, with labels being renamed even substantially across releases. While this helps reveal newer aspects on the classification of viruses, existing bioinformatic methods for classification struggle to stay in sync with this ever-improving resource.</p><p><strong>Results: </strong>We developed a new computer program, named VIRGO, that is able to correctly predict virus families from metagenomic data with an F1 score above 0.9 using a novel viral sequence similarity metric proposed in this work. Moreover, it ensures compatibility with any version of the official taxonomy of viruses.</p><p><strong>Conclusions: </strong>Virgo is designed to easily incorporate newer releases of the official taxonomy, thus representing a valuable resource in the virology community while raising awareness to develop computational methods that evolve alongside manually curated resources. Video Abstract.</p>\",\"PeriodicalId\":18447,\"journal\":{\"name\":\"Microbiome\",\"volume\":\"13 1\",\"pages\":\"170\"},\"PeriodicalIF\":12.7000,\"publicationDate\":\"2025-07-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12291348/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Microbiome\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s40168-025-02159-x\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbiome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s40168-025-02159-x","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
Bidirectional subsethood of shared marker profiles enables accurate virus classification.
Background: Due to the impact of viral metagenomic sequencing, the official virus taxonomy is updated several times a year, with labels being renamed even substantially across releases. While this helps reveal newer aspects on the classification of viruses, existing bioinformatic methods for classification struggle to stay in sync with this ever-improving resource.
Results: We developed a new computer program, named VIRGO, that is able to correctly predict virus families from metagenomic data with an F1 score above 0.9 using a novel viral sequence similarity metric proposed in this work. Moreover, it ensures compatibility with any version of the official taxonomy of viruses.
Conclusions: Virgo is designed to easily incorporate newer releases of the official taxonomy, thus representing a valuable resource in the virology community while raising awareness to develop computational methods that evolve alongside manually curated resources. Video Abstract.
期刊介绍：
Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.
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