Literature DB >> 33546975

Microbial Taxonomy Run Amok.

Robert A Sanford1, Karen G Lloyd2, Konstantinos T Konstantinidis3, Frank E Löffler4.   

Abstract

DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. We exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Keywords:  Geobacter; Pelobacter; codes of nomenclature; metagenome-assembled genomes; not-yet-cultured microorganisms; prokaryotic taxonomy

Year:  2021        PMID: 33546975     DOI: 10.1016/j.tim.2020.12.010

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  9 in total

Review 1.  The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies.

Authors:  Jina Rajkumari; Prashant Katiyar; Shrivardhan Dheeman; Piyush Pandey; Dinesh Kumar Maheshwari
Journal:  World J Microbiol Biotechnol       Date:  2022-08-26       Impact factor: 4.253

2.  New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient.

Authors:  Miguel Angel Cevallos; Mauro Degli Esposti
Journal:  Microorganisms       Date:  2022-02-16

3.  Could a Focus on the "Why" of Taxonomy Help Taxonomy Better Respond to the Needs of Science and Society?

Authors:  Leighton Pritchard; C Titus Brown; Bailey Harrington; Lenwood S Heath; N Tessa Pierce-Ward; Boris A Vinatzer
Journal:  Front Microbiol       Date:  2022-05-19       Impact factor: 6.064

4.  Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.

Authors:  Camila Gazolla Volpiano; Fernando Hayashi Sant'Anna; Adriana Ambrosini; Jackson Freitas Brilhante de São José; Anelise Beneduzi; William B Whitman; Emanuel Maltempi de Souza; Bruno Brito Lisboa; Luciano Kayser Vargas; Luciane Maria Pereira Passaglia
Journal:  Front Microbiol       Date:  2021-03-25       Impact factor: 5.640

5.  Using Cartesian Doubt To Build a Sequencing-Based View of Microbiology.

Authors:  Braden T Tierney; Erika Szymanski; James R Henriksen; Aleksandar D Kostic; Chirag J Patel
Journal:  mSystems       Date:  2021-10-12       Impact factor: 7.324

Review 6.  The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.

Authors:  Mark J Pallen
Journal:  Int J Syst Evol Microbiol       Date:  2021-09       Impact factor: 2.747

7.  Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping.

Authors:  Adyasha Panda; Salim T Islam; Gaurav Sharma
Journal:  mBio       Date:  2022-05-10       Impact factor: 7.786

8.  Desulfuromonas sp. 'CSMB_57', isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals.

Authors:  Andrew G McLeish; Paul Greenfield; David J Midgley; Ian T Paulsen
Journal:  Microb Genom       Date:  2022-08

9.  Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters.

Authors:  Patrick D Schloss
Journal:  mSphere       Date:  2021-07-21       Impact factor: 4.389

  9 in total

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