Abstract
Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.
Highlights
Microorganisms are considered the most abundant organisms in the world
As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status
For the new species identification pipeline, the new type strain genome sequence is used as the query in a similarity search against the Global Catalogue of Type Strain (gcType) 16S rRNA gene and genome sequence reference database following the recommendations for the use of genome data in International Journal of Systematic and Evolutionary Microbiology (IJSEM)
Summary
Microorganisms are considered the most abundant organisms in the world. It is estimated that ∼4–6 × 1030 prokaryotic cells exist on Earth, comprising a biomass of 350–550 × 1015 g of carbon [1]. The information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a highquality reference database.
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