Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources

Abstract

Background: Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities.

Description: Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436 bacterial, fungal and archaea species from 52 collections in 25 countries and regions.A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM.

Conclusion: A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the activities of microbiologists world-wide, who work in both public and industrial research centres. This database is available from http://gcm.wfcc.info.

Figure 1

Scheme of the workflow of GCM. Catalogue information from each of collection, shown on the left, is used to construct the framework of the global catalogue database. Species name and strain numbers are collected from the catalogue information, and are further used to identify and extract information from public database such as Genbank, NCBI Genome, SwissProt, PDB, Pubmed and the patent database. The data warehouse is built in a SQL database, and can be accessed via a web interface through different search options. Search results may be displayed in different formats allowing users to refine the results by using filters. The final results are displayed either as a strain page or they can be gathered into a species page depending on the query. BLAST and ClustalW are provided for further analysis of the results.

Figure 2

Example of Species page of Lactobacillus delbrueckii subsp. bulgaricus.

Figure 3

Example of strain information of Lactobacillus delbrueckii subsp. bulgaricus.

Figure 4

Database management system for collections. Users can import data by generating an EXCEL file to meet the WDCM RDS. After the data are imported into the system, users can either update or edit the catalogue information online. A species name check result is provided in the database management system to provide an overview of data quality and allow for further modifications.