CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
Chemical.AI Wuhan, Wuhan, 430062, China.
Microb Cell Fact. 2022 May 14;21(1):87. doi: 10.1186/s12934-022-01813-5.
Microbial strain information databases provide valuable data for microbial basic research and applications. However, they rarely contain information on the genetic operating system of microbial strains.
We established a comprehensive microbial strain database, SynBioStrainFinder, by integrating CRISPR/Cas gene-editing system information with cultivation methods, genome sequence data, and compound-related information. It is presented through three modules, Strain2Gms/PredStrain2Gms, Strain2BasicInfo, and Strain2Compd, which combine to form a rapid strain information query system conveniently curated, integrated, and accessible on a single platform. To date, 1426 CRISPR/Cas gene-editing records of 157 microbial strains have been manually extracted from the literature in the Strain2Gms module. For strains without established CRISPR/Cas systems, the PredStrain2Gms module recommends the system of the most closely related strain as a reference to facilitate the construction of a new CRISPR/Cas gene-editing system. The database contains 139,499 records of strain cultivation and genome sequences, and 773,298 records of strain-related compounds. To facilitate simple and intuitive data application, all microbial strains are also labeled with stars based on the order and availability of strain information. SynBioStrainFinder provides a user-friendly interface for querying, browsing, and visualizing detailed information on microbial strains, and it is publicly available at http://design.rxnfinder.org/biosynstrain/ .
SynBioStrainFinder is the first microbial strain database with manually curated information on the strain CRISPR/Cas system as well as other microbial strain information. It also provides reference information for the construction of new CRISPR/Cas systems. SynBioStrainFinder will serve as a useful resource to extend microbial strain research and application for biomanufacturing.
微生物菌株信息数据库为微生物基础研究和应用提供了有价值的数据。然而，它们很少包含关于微生物菌株遗传操作系统的信息。
我们通过整合 CRISPR/Cas 基因编辑系统信息与培养方法、基因组序列数据和化合物相关信息，建立了一个综合的微生物菌株数据库 SynBioStrainFinder。它通过三个模块呈现，Strain2Gms/PredStrain2Gms、Strain2BasicInfo 和 Strain2Compd，它们结合在一起形成了一个快速的菌株信息查询系统，方便在单个平台上进行编辑、集成和访问。迄今为止，Strain2Gms 模块已从文献中手动提取了 157 株微生物菌株的 1426 个 CRISPR/Cas 基因编辑记录。对于尚未建立 CRISPR/Cas 系统的菌株，PredStrain2Gms 模块推荐最密切相关菌株的系统作为参考，以方便构建新的 CRISPR/Cas 基因编辑系统。该数据库包含 139499 条菌株培养和基因组序列记录，以及 773298 条菌株相关化合物记录。为了方便简单直观的数据应用，所有微生物菌株也根据菌株信息的顺序和可用性进行了星级标记。SynBioStrainFinder 为查询、浏览和可视化微生物菌株的详细信息提供了用户友好的界面，它可在 http://design.rxnfinder.org/biosynstrain/ 上公开获取。
SynBioStrainFinder 是第一个具有手动编辑的菌株 CRISPR/Cas 系统信息以及其他微生物菌株信息的微生物菌株数据库，它还为构建新的 CRISPR/Cas 系统提供了参考信息。SynBioStrainFinder 将成为扩展微生物菌株研究和应用于生物制造的有用资源。
