Type Strain Genome Server
TYGS primer

Microorganisms heavily influence life on earth more than any other group of organisms and hold all records with respect to abundance, biomass, genetic diversity and diversity of metabolic pathways. The classification, characterization and identification of microbes is of utmost importance for medicine, biotechnology and ecology. To validly publish a new species name, the deposition of the respective type strain in culture collections is required, which guarantees an unrestricted access to life samples for the scientific community. Today, the tremendous advances in sequencing technologies call for considering genome sequencing as a novel standard technique for the characterization of microorganisms.

The Type (Strain) Genome Server (TYGS) closes a gap by providing a publicly available bioinformatics infrastructure. It builds on the established GGDC infrastructure but adds a variety of taxonomically useful facilities. TYGS allows for a genome-based replacement of taxonomic standard techniques such as DNA:DNA hybridization (DDH), G+C-content measurement, 16S rRNA gene sequencing and multi-locus sequence analysis. TYGS results include species and subspecies boundaries, genome-scale, proteome-scale (optional) and 16S rRNA gene phylogenetic trees with branch support, links to the taxonomic literature and links to deposits of type strains in culture collections (please find an example here). The relevant type-strain genomes are determined automatically but can also be specified by the user.

In summary, TYGS ...
  • ... is the successor of the popular Genome-to-Genome Distance Calculator (~3.6K citations as of 01/22), an online tool for the calculation of digital DDH values for in silico (sub-)species delineation.
  • ... is a user-friendly high-throughput web server for genome-based prokaryote taxonomy
  • ... is connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information
  • ... is highly interconnected with the LPSN database and depends on its expert-curated nomenclatural data
  • ... provides a multitude of tailored results such as genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences
  • ... provides comprehensive access to nomenclature, synonymy and associated taxonomic literature
TYGS basic workflow

TYGS workflow

Dependencies between TYGS and LPSN databases

Dependencies between TYGS and LPSN databases

Figure shows the dependencies between the TYGS and LPSN databases. As expected for these two highly interconnected platforms, the broadening of the scope of names included in LPSN automatically also broadens the scope of genome sequences found in the TYGS. Figure from Meier-Kolthoff et al., Nucleic Acids Res. 50, D801–D807 (2022).

How to cite TYGS in your upcoming publication