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

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.

Fig. 1

Statistical summary of the SynBioStrainFinder database. a Main data in SynBioStrainFinder, including species number (SN), species with culture medium (SCM), sequenced species (SS), species with reported compounds (SC), and species with CRISPR/Cas systems (SCS). b Proportions of publications reporting four gene-editing methods (zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), Cre/loxp, and CRISPR/Cas) annually. c CRISPR/Cas system construction and delivery type. d Frequently used promoters for Cas9 and sgRNA expression. *, corresponding promoter and its deformation. e Homologous arm length of donor DNA for HDR. f Commonly used sgRNA design tools. g CRISPR/Cas system gene-editing type. h Top 10 species with high strain-related compound counts

Fig. 2

Application of SynBioStrainFinder data. a Example of star-tags for strains in SynBioStrainFinder. All microbial strains were marked with stars according to the order and extent of information available on strain cultivation, genome sequence, CRISPR/Cas genetic operating system, and related compounds. b Application of star-tags to host organism selection with CF-targeter. The strain star-tag can be added next to the strain list

Fig. 3

Database content and interface of SynBioStrainFinder. The database consists of three modules: a Strain2BasicInfo module for strain cultivation and genome sequence, b Strain2Gms/PredStrain2Gms module for CRISPR/Cas genetic operating system, and c Strain2Compd module for related compounds. The top of the browse-results page shows statistical information for the Strain2Gms and Strain2Compd modules and the phylogenetic tree for the Strain2BasicInfo module. d–j The bottom of the browse-results page contains detailed information, which can be expanded further