Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy

Abstract

We recently introduced the Genome Taxonomy Database (GTDB), a phylogenetically consistent, genome-based taxonomy providing rank normalized classifications for nearly 150,000 genomes from domain to genus. However, nearly 40% of the genomes used to infer the GTDB reference tree lack a species name, reflecting the large number of genomes in public repositories without complete taxonomic assignments. Here we address this limitation by proposing 24,706 species clusters which encompass all publicly available bacterial and archaeal genomes when using commonly accepted average nucleotide identity (ANI) criteria for circumscribing species. In contrast to previous ANI studies, we selected a single representative genome to serve as the nomenclatural type for circumscribing each species with type strains used where available. We complemented the 8,792 species clusters with validly or effectively published names with 15,914 de novo species clusters in order to assign placeholder names to the growing number of genomes from uncultivated species. This provides the first complete domain to species taxonomic framework which will improve communication of scientific results. taxonomic framework where genomes have assignments at all ranks from domain to species (Parks et al., 2018).

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

“…In those studies, genomes most commonly shared either Ͼ97% or Ͻ90% average nucleotide identity (ANI). A bacterial species threshold of 95% ANI, originally proposed on the basis of benchmarking with respect to DNA-DNA hybridization values (8), has been gaining increasing support (11) on the basis of that observation. However, it is still unclear whether this pattern is confounded by database biases or whether it reflects a true phenomenon across natural environments, as comparisons of phylogenetically unbalanced genome sets could result in the formation of spurious sequence clusters.…”

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds

“…Genomes were classified using the standalone GTDB-Tk tool (version 0.3.2) using the classify workflow and the Genome Taxonomy Database version 89 [24]. The tool appears unable to classify genomes less than 10% complete, as indicated in the respective tables.…”

“…Genomes carrying fewer than 6 genes (cumulative) in these two categories were collapsed. Phylogeny was inferred using JolyTree [24] with a sketch size of 5 000. Conserved genomes are indicated with an asterisk within highlighted taxonomic groups.…”

Diversity and Host Interactions among Virulent and Temperate Baltic Sea Flavobacterium Phages

“…GTDBtk (version 0.3.2) [70] was used to place the bacterial genomes of LMO6, LMO8 and LMO9 in the Genome Taxonomy Database [71] tree, which was conducted through analysis of a set of marker genes, and calculate shared average nucleotide identity with the reference genomes. The tree was visualised with Dendroscope (version 3.5.9) [72].…”

“…Phylogenomic placement of the three strains from this study-LMO6, LMO8, and LMO9-in the GTDB phylogeny[71]. The three strains were placed with GTDBtk[70] and here visualised together with their closest Flavobacterium spp.…”