Microbial Taxonomy Run Amok

Robert A.Sanford¹, Karen G.Lloyd², Konstantinos T.Konstantinidis³, Frank E.Löffler^2,4,5,6,7

Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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.

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