SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing

Pengli Cai; Mengying Han; Rui Zhang; Shaozhen Ding; Dachuan Zhang; Dongliang Liu; Sheng Liu; Qian-Nan Hu

doi:10.1186/s12934-022-01813-5

SynBioStrainFinder: A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing

Microb Cell Fact. 2022 May 14;21(1):87. doi: 10.1186/s12934-022-01813-5.

Authors

Pengli Cai^#¹, Mengying Han^#¹, Rui Zhang¹, Shaozhen Ding², Dachuan Zhang¹, Dongliang Liu¹, Sheng Liu¹, Qian-Nan Hu³

Affiliations

¹ 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.
² Chemical.AI Wuhan, Wuhan, 430062, China.
³ 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. qnhu@sibs.ac.cn.

^# Contributed equally.

Abstract

Background: 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.

Results: 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/ .

Conclusion: 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.

Keywords: CRISPR/Cas system; Database; Gene-editing method; Genome sequence; Microorganism; Strain cultivation; Strain-related compound.

MeSH terms

CRISPR-Cas Systems*
Gene Editing*

Abstract

MeSH terms

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