19-BBSRC-NSF/BIO genomeRxiv: a microbial whole-genome database & diagnostic marker design resource for classification, identification & data sharing

19-BBSRC-NSF/BIOgenomeRxiv：微生物全基因组数据库

• 批准号: BB/V010417/1
• 负责人: Leighton Pritchard
• 金额: $ 45.13万
• 依托单位: University of Strathclyde
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FV010417%2F1
• 关键词: 19; BBSRC; NSF; BIO; genomeRxiv

Precise identification of microorganisms that impact on society and the environment is a prerequisite for maintaining a healthy society and a healthy environment and for combating diseases, in addition to providing a sound empirical core for understanding microbiology. The DNA sequencing revolution has created the opportunity to use genome sequences of cultured and uncultured microorganisms for fast and precise identification. However, precise identification is impossible without reference databases that precisely circumscribe classes of microorganisms with their unique characteristics, and rapid identification is impossible without fast algorithms that can handle the deluge of genome sequences being sequenced. Therefore, we will enhance our current web server to develop genomeRxiv, which will provide a database of hundreds of thousands of accurately catalogued and classified public genome sequences supplying the basic and applied research community with precise and accurate identification of unknown isolates based on their genome sequences alone.A unique new feature will be provision of the academic, industrial, and government communities with the ability to identify, and announce, sequenced genomes without having to share sequences themselves, providing confidentiality for commercially- and ethically-sensitive organisms (e.g. production engineering strains, potential bioweapons, and benefit sharing with indigenous communities). genomeRxiv will also enable practical application of its classification scheme by providing the capability to design molecular diagnostic tools to detect specific groupings of bacteria, including high impact microorganisms, directly in the environment.We are uniquely placed to develop genomeRxiv by leveraging the computational tools and platforms that we have already developed and by integrating them into the new web server. We will combine the highly-resolved classification framework of Life Identification Numbers (PIs Vinazter and Heath), the speed and computational efficiency of sourmash (PI Brown), and the precision and filtering of pyani (PI Pritchard), with the collaborative crowdsourcing framework of the LINbase web server (PIs Vinazter and Heath).

除了为理解微生物学提供可靠的经验核心外，准确查明对社会和环境有影响的微生物是维持健康的社会和健康的环境以及防治疾病的先决条件。DNA测序革命创造了利用培养和未培养微生物的基因组序列进行快速精确鉴定的机会。然而，如果没有参考数据库精确地限定具有独特特征的微生物类别，就不可能进行精确鉴定，而如果没有能够处理大量基因组序列的快速算法，就不可能进行快速鉴定。因此，我们将改进现有的web服务器来开发genomeRxiv，它将提供数十万个准确编组和分类的公共基因组序列的数据库，为基础和应用研究界提供仅基于基因组序列的未知分离物的精确和准确鉴定。一个独特的新功能将是为学术、工业和政府团体提供识别和宣布测序基因组的能力，而不必共享序列本身，为商业和伦理敏感的生物体（例如生产工程菌株、潜在的生物武器和与土著社区分享利益）提供机密性。genomeRxiv还将提供设计分子诊断工具的能力，以直接在环境中检测特定的细菌分组，包括高影响微生物，从而使其分类方案的实际应用成为可能。通过利用我们已经开发的计算工具和平台，并将它们集成到新的web服务器中，我们在开发genomeRxiv方面处于独特的地位。我们将把生命识别号的高分辨率分类框架（PI Vinazter和Heath）、sourmash的速度和计算效率（PI Brown）、pyani的精度和过滤（PI Pritchard）与LINbase web服务器的协作众包框架（PI Vinazter和Heath）结合起来。

项目成果

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces

• DOI: 10.1101/2023.08.15.553377
• 发表时间: 2023-08
• 期刊: bioRxiv
• 作者: Angelika B Kiepas;P. Hoskisson;L. Pritchard

Could a Focus on the "Why" of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society?

关注分类学的“为什么”可以帮助分类学更好地响应科学和社会的需求吗？

• DOI: 10.20944/preprints202203.0069.v1
• 发表时间: 2022
• 作者: Pritchard L

LINgroups as a principled approach to compare and integrate multiple bacterial taxonomies

LINgroups 作为比较和整合多种细菌分类法的原则方法

• DOI: 10.1145/3535508.3545546
• 发表时间: 2022
• 期刊: Computational Biology and Health Informatics
• 作者: Mazloom, Reza;Pritchard, Leighton;Brown, C. Titus;Vinatzer, Boris A.;Heath, Lenwood S.
• 通讯作者: Heath, Lenwood S.