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

Mark J Pallen

doi:10.1099/ijsem.0.005000

Abstract

The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.

Highlights

The International Code for Nomenclature of Prokaryotes articulates principles, rules and recommendations for the naming of archaeal and bacterial taxa, including rules for the valid publication of names and establishing priority in the literature [1]
We described 657 Candidatus species names and 158 Candidatus genera names in a series of protologues that occupied over 100 pages of the paper [37]
Lacking priority under the code, many Candidatus names have already achieved standing in the academic literature and in key databases and there is a clear path to valid publication of such names on culture

Summary

INTRODUCTION

The International Code for Nomenclature of Prokaryotes (the ICNP or ‘the Code’) articulates principles, rules and recommendations for the naming of archaeal and bacterial taxa, including rules for the valid publication of names and establishing priority in the literature [1]. The committee agreed that a ‘Candidatus name is by definition a preliminary name and has no standing in prokaryote nomenclature’, they were happy to incorporate the Candidatus option within an appendix within the Code and suggested that a list of organisms with the status Candidatus should maintained and published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) at appropriate intervals [1, 11] In parallel with these developments, the Committee discussed and mandated a requirement that valid publication of names required deposition of viable pure cultures in strain repositories in two countries, which came into effect from 1 January 2001 [1, 11, 12]. This list was compiled by downloading the genera, species and subspecies list from the List of Prokaryotic names with Standing in Nomenclature (https://lpsn.dsmz.de/downloads) and sorting and selecting entries by nomenclatural type

Wolbachia melophagi Wolbachia pipientis

CONCLUSIONS