Scientific Background

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.

• ... 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

The publications describing the Type (Strain) Genome Server (TYGS) and its subsequent updates and feature additions
• Meier-Kolthoff J.P., Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10:2182, 2019. [Citations]
• Meier-Kolthoff J.P., Sardà Carbasse J., Peinado-Olarte R.L., Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acid Res 50:D801–D807, 2022. [Citations]

Genome BLAST Distance Phylogeny approach (GBDP)
• Henz, S.R., Huson, D.H., Auch, A.F., Nieselt-Struwe, K., Schuster, S.C. Whole-genome prokaryotic phylogeny. Bioinformatics 21:2329-2335, 2005. [Citations]
• Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.-P., Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60, 2013. [Citations]
• Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.-P., Göker, M. Highly parallelized inference of large genome-based phylogenies. Concurr Comput Pr Exper (Special Issue) 26:1715-1729, 2014. [Citations]
• Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.-P., Göker, M. GBDP on the grid: a genome-based approach for species delimitation adjusted for an automated and highly parallel processing of large data sets. pp. 83-102 In: Schulz J, Hermann S (eds) Hochleistungsrechnen Baden-Württemb. – Ausgewählte Aktivitäten im bwGRiD 2012. KIT Scientific Publishing, Karlsruhe, 2014. [Citations]
• Auch, A.F., Henz, S.R., Holland, B., Göker, M. Genome blast distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinformatics 7: 350, 2006. [Citations]
• Auch, A.F., Henz. S.R., Göker, M. Phylogenies from whole genomes - Methodological update within a distance-based framework. German conference on Bioinformatics, Tübingen 2006. Published online via tobias-lib.

Genome-based species delimitation via GBDP
• Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.-P., Göker, M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60, 2013. [Citations]
• Auch, A.F., Klenk, H.-P., Göker, M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Standards in Genomic Sciences 2:142-148, 2010. [Citations]
• Auch, A.F., Von Jan, M., Klenk, H.-P., Göker, M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Standards in Genomic Sciences 2:117-134, 2010. [Citations]

Genome-based subspecies delimitation via GBDP
• Meier-Kolthoff, J.P., Hahnke, R.L., Petersen, J., Scheuner, C., Michael, V., Fiebig, A., Rohde, C., Rohde, M., Fartmann, B., Goodwin, L.A., Chertkov, O., Reddy, T., Pati, A., Ivanova, N.N., Markowitz, V., Kyrpides, N.C., Woyke, T., Göker, M., Klenk, H-P. Complete genome sequence of DSM 30083^T, the type strain (U5/41^T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Standards in Genomic Sciences 10:2, 2014. [Citations]

How and why the differences in genomic G+C content can be used for species delineation
• Meier-Kolthoff, J.P., Göker, M., Klenk, H.-P. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352-356, 2014. [Citations]

Selection of phylogenomic and taxonomic studies making of use of GBDP and other methods listed above.
• Hördt, A., García-López, M., Meier-Kolthoff, J. P., Schleuning, M., Weinhold, L. M., Tindall, B. J., et al. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 11:468, 2020.
• García-López, M., Meier-Kolthoff, J. P., Tindall, B. J., Gronow, S., Woyke, T., Kyrpides, N. C., et al. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 10:2083, 2019.
• Nouioui, I., Carro, L., García-López, M., Meier-Kolthoff, J. P., Woyke, T., Kyrpides, N., Pukall, R., Klenk, H.-P., Goodfellow, M., Göker, M. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 9:1-119, 2018.
• Hahnke, R. L., Meier-Kolthoff, J. P., García-López, M., Mukherjee, S., Huntemann, M, Ivanova, N. N., Woyke, T., Kyrpides, N. C., Klenk, H.-P., Göker, M. Genome-Based Taxonomic Classification of Bacteroidetes. Front Microbiol 7:2013, 2017.
• Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe-Fadrosh, E. A., Meier-Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Paez-Espino, D., Yoshikuni, Y., Visel, A., Whitman, W. B., Garrity, G. M., Eisen, J. A., Hugenholtz, P., Pati, A., Ivanova, N. N., Woyke, T., Klenk, H.-P., Kyrpides, N. C. 1,003 Reference Genomes of Bacterial and Archaeal Isolates Expand Coverage of the Tree of Life. Nat Biotechnol 35:676-683, 2017.
• Riley, R., Haridas, S., Wolfe, K.H., Lopes, M.R., Hittinger, CT., Göker, M., Salamov, A., Wisecaver, J., Long, T.M., Aerts, A.L., Choi, C., Clum, A., Coughlan, A.Y., Deshpande, S., Alexander, P., Hanson, S.J., Klenk, H.-P., Labutti, K., Lapidus, A., Lindquist, E., Lipzen, A., Meier-Kolthoff, J.P., Ohm, R.A., Otillar, R.P., Pangilinan, J., Rokas, A., Rosa, C.A., Scheuner, C., Sibirny, A., Slot, JC., et, al. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci 113:9882-9887, 2016.
• Lagkouvardos, I., Pukall, R., Abt, B., Foesel, B.U., Meier-Kolthoff, J.P., Kumar, N., Bresciani, A., Martínez, I., Just, S., Ziegler, C., Brugiroux, S., Garzetti, D., Wenning, M., Bui, T.P.N., Wang, J., Hugenholtz, F., Plugge, C.M., Peterson, D.A., Hornef, M.W., Baines, J.F., Smidt, H., Walter, J., Kristiansen, K., Nielsen, H.B., Haller, D., Overmann, J., Stecher, B., Clavel, T. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 1:16131, 2016.
• Peeters, C., Meier-Kolthoff, J.P., Verheyde, B., De Brandt, E., Cooper, V.S., Vandamme, P. Phylogenomic Study of Burkholderia glathei-like organisms, proposal of 13 novel Burkholderia species and emended descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae. Front Microbiol 7:1-19, 2016.
• Garrido-Sanz, D., Meier-Kolthoff, J.P., Göker, M., Martin, M., Rivilla, R., Redondo-Nieto, M. Genomic and genetic diversity within the Pseudomonas fluorescens complex. PLoS ONE 11:e0150183, 2016.
• Liu, Y., Lai, Q., Göker, M., Meier-Kolthoff, J.P., Wang, M., Sun, Y., Wang, L., Shao, Z. Genomic insights into the taxonomic status of the Bacillus cereus group. Scientific Reports 5:14082, 2015.