GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Abstract

The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.

Comparative Analysis of anti-Shine- Dalgarno Function in Flavobacterium johnsoniae and Escherichia coli

“…Thus, the autoregulatory mechanism seems no less common in the Bacteroidia. Supplementary Figure S3 shows occurrences of programmed frameshifting projected onto the GTDB phylogenetic tree ( Parks et al, 2021 ). The frameshift is present in all Sphingobacteriales analyzed and absent from all Weeksellaceae analyzed.…”

“…A list of 997 organisms from the orders Cytophagales, Bacteroidales, Chitinophagales, Flavobacteriales, and Sphingobacteriales marked as GTDB species representatives and as NCBI type material were downloaded from GTDB ( Parks et al, 2021 ) (Table S2). 740 of these genome assemblies were successfully downloaded and ARFA ( Bekaert et al, 2006 ) was run on these assemblies with default parameters.…”

“…downloaded from GTDB (Parks et al, 2021) (Table S2). 740 of these genome assemblies were successfully downloaded and ARFA (Bekaert et al, 2006) was run on these assemblies with default parameters.…”

Naming the Unnamed: Over 45,000 Candidatus Names for Unnamed Archaea and Bacteria in the Genome Taxonomy Database

“…However, the provisional status of the names proposed here can be seen as helpful, in that if, in the future, those working on a given taxon wish to propose a new name, they are perfectly entitled to do so within the current system-albeit with the proviso that the opening principle of the ICNP is to "aim for stability in names". Aside from such changes, the vast majority of the Candidatus names proposed here are likely to remain highly stable-given that only 0.26% of genomes are on average assigned to a different species cluster from one release of GTDB to the next [7]-and so can now be safely adopted by databases and used in the scientific literature.…”

“…CG2-30-70-394), selected arbitrarily from identifiers in public sequence databases. These unnamed placeholder taxa now clearly outnumber those with names: in the latest release of the GTDB taxonomy [7] around a quarter of species (12,398 or 25.9%) have been assigned Latin names, while roughly three quarters of the species (35,496 or 74.1%) are identified only by alphanumeric placeholders labels.…”