gcType: a high-quality type strain genome database for microbial phylogenetic and functional research

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/.

Classification of a Violacein-Producing Psychrophilic Group of Isolates Associated with Freshwater in Antarctica and Description of Rugamonas violacea sp. nov.

“…The de novo WGS analysis was performed for the detailed taxonomic characterization of P5900 T . The whole-genome sequencing and its annotation were carried out in the framework of the Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project as described previously ( 33 , 34 ). The whole-genome sequence of P5900 T (GenBank accession JAEMNU000000000 ) was compared to those of the related Rugamonas rubra ATCC 43154 T (GenBank accession FOTW00000000 ), Rugamonas aquatica GDMCC 1.1643 T (GenBank accession WHUG00000000 ), and Rugamonas rivuli GDMCC 1.1685 T (GenBank accession WHUF00000000 ) obtained from the NCBI database.…”

Molecular Analysis of bla KPC-2 -Harboring Plasmids: Tn 4401a Interplasmid Transposition and Tn 4401a -Carrying ColRNAI Plasmid Mobilization from Klebsiella pneumoniae to Citrobacter europaeus and Morganella morganii in a Single Patient

“…MiSeq output reads were assembled with SPAdes v3.13.1 ( 33 ). Species identification was performed using the ANI with the type strain database gcType ( 34 ) and the comparesketch command in the BBMap package ( https://sourceforge.net/projects/bbmap/ ) ( 35 ). We used a cutoff value of ≥96% ( 36 ) of the ANI value compared with the genomic sequences of the type strain for species identification.…”

Characterization and Genome Analysis of Arthrobacter bangladeshi sp. nov., Applied for the Green Synthesis of Silver Nanoparticles and Their Antibacterial Efficacy against Drug-Resistant Human Pathogens

“…The common features of the genome sequence of strain MAHUQ-56 T are shown in Table 2. Characterization of novel species is increasingly dependent on genomic sequence [37]. Functional annotation by the RAST server showed that 172 genes were involved with the metabolism of proteins, 83 genes were associated with the metabolism of nucleosides and nucleotides, 343 genes were linked with amino acids and derivatives, and 408 genes were involved with carbohydrate metabolism (Figure 3).…”