Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing.
Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing.
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使用 VEBA 2.0 揭开微生物领域的面纱：模块化生物信息学套件，用于通过短读长或长读长测序进行端到端基因组解析的原核生物、（微）真核生物和病毒多组学。
DOI：
10.1101/2024.03.08.583560
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Dupont,ChrisL
中科院分区：
文献类型：
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作者：
Espinoza,JoshL;Phillips,Allan;Prentice,MelanieB;Tan,GeneS;Kamath,PaulineL;Lloyd,KarenG;Dupont,ChrisL
微生物组是微生物的复杂群落，包括原核生物（细菌和古细菌）、真核生物和病毒实体。这种微生物群落在影响不同生态系统的健康和生产力方面发挥着关键作用，同时塑造了生命网络。然而，许多开发用于研究微生物组的软件套件仅分析原核生物群落，并对病毒和微真核生物提供有限的支持。在此之前，我们引入了病毒真核生物细菌学（VEBA）开源软件套件，通过将基因组解析分析扩展到原核生物之外，以涵盖真核生物和病毒的未充分研究领域，来解决微生物组研究中的这一关键空白。在这里，我们介绍了VEBA 2.0的关键更新，包括一个全面的聚类微真核蛋白质数据库，快速基因组/蛋白质水平聚类，生物勘探，非编码/细胞器基因建模，基因组分辨分类/途径分析，长读支持，和集装箱化。我们通过分析不同的案例研究，包括海水，西伯利亚永久冻土和白尾鹿肺组织，展示了VEBA的多功能应用，后者展示了如何识别整合病毒。VEBA代表了微生物组研究的重要进展，提供了一个强大且易于使用的软件套件，弥合了基因组学和生物技术解决方案之间的差距。
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced theViral Eukaryotic Bacterial Archaeal(VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we presentVEBA 2.0with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrateVEBA’sversatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses.VEBArepresents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.