1
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database

      1 , 2 , 3 , 4 , 5 , 1
      International Journal of Systematic and Evolutionary Microbiology
      Microbiology Society

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

          Related collections

          Most cited references34

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

          Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10 156 bacterial and archaeal metagenome-assembled genomes. Availability and implementation GTDB-Tk is implemented in Python and licenced under the GNU General Public Licence v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk. Supplementary information Supplementary data are available at Bioinformatics online.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

            Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              A complete domain-to-species taxonomy for Bacteria and Archaea

              The Genome Taxonomy Database is a phylogenetically consistent, genome-based taxonomy that provides rank-normalized classifications for ~150,000 bacterial and archaeal genomes from domain to genus. However, almost 40% of the genomes in the Genome Taxonomy Database lack a species name. We address this limitation by using commonly accepted average nucleotide identity criteria to set bounds on species and propose species clusters that encompass all publicly available bacterial and archaeal genomes. Unlike previous average nucleotide identity studies, we chose a single representative genome to serve as the effective nomenclatural 'type' defining each species. Of the 24,706 proposed species clusters, 8,792 are based on published names. We assigned placeholder names to the remaining 15,914 species clusters to provide names to the growing number of genomes from uncultivated species. This resource provides a complete domain-to-species taxonomic framework for bacterial and archaeal genomes, which will facilitate research on uncultivated species and improve communication of scientific results.
                Bookmark

                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                International Journal of Systematic and Evolutionary Microbiology
                Microbiology Society
                1466-5026
                1466-5034
                September 20 2022
                September 20 2022
                : 72
                : 9
                Affiliations
                [1 ] Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
                [2 ] Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
                [3 ] School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
                [4 ] Digital Science Center, University of Innsbruck, Innsbruck, Tyrol, Austria
                [5 ] Department of Microbiology, University of Innsbruck, Innsbruck, Tyrol, Austria
                Article
                10.1099/ijsem.0.005482
                a0b18f72-fc44-49a9-8853-b415deb61c56
                © 2022

                http://creativecommons.org/licenses/by/4.0/

                History

                Comments

                Comment on this article