Abstract
Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Here we introduce TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy, connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information. It infers genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries from user-defined and automatically determined closest type genome sequences. TYGS also provides comprehensive access to nomenclature, synonymy and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of Salmonella enterica. TYGS is an integrated approach for the classification of microbes that unlocks novel scientific approaches to microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species or subspecies.
Highlights
Microbial taxonomy is increasingly influenced by genome-based computational methods
Hybridization over genotypic analyses (e.g., 16S rRNA) to analyses of whole genomes. Even though these methods can contribute toward the taxonomic positioning of samples, bacterial taxonomy is nowadays increasingly influenced by genome-based approaches[5]
Whereas conventional DNA:DNA hybridization (DDH) and G+C content measurement are known[6,7] to be rather error-prone, tedious and only available in specialized laboratories, their genome-based counterparts provide a new level of standardization due to instant reproducibility and validation, yielding a huge gain in time and methodological accuracy[7]
Summary
Microbial taxonomy is increasingly influenced by genome-based computational methods. Yet such analyses can be complex and require expert knowledge. Since the late 19th century, technological advances have continuously influenced taxonomic procedures and techniques[4], ranging from analyses on morphology, physiology and biochemistry, chemotaxonomy, numerical taxonomy, DNA G+C content, DNA:DNA hybridization (DDH), and DNA:rRNA hybridization over genotypic analyses (e.g., 16S rRNA) to analyses of whole genomes. Even though these methods can contribute toward the taxonomic positioning of samples, bacterial taxonomy is nowadays increasingly influenced by genome-based approaches[5]. Phylogenetic analyses of the 16S rRNA gene sequence[4] nowadays still heavily contribute to our understanding of prokaryotic systematics, but these are incapable of unambiguously resolving evolutionary relationships within many groups[4]
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