Leveraging the subgenus category to address genus over-splitting exemplified with Prescottella and other recently proposed Mycobacteriales genera

ABSTRACT Three related circumstances are compromising the stability of prokaryotic taxonomy and nomenclature, with a significant impact in the field of pathogenic microorganisms: (i) the growing trend of subdividing existing genera by arbitrary phylogenomics-based demarcations, creating an increasing number of new genera; (ii) the priority of databases towards the last validly published names; and (iii) the irreversibility of new names in databases even if changes in taxonomic opinion support reverting to previous classifications. Given the understandable end-user reluctance to name changes affecting well-known pathogens, parallel nomenclatures coexist, creating confusion. Here, we address this problem by exploiting the subgenus category to form new combinations that can be adopted by databases as per their latest validly published name priority policy. The proposed approach consists in lowering to subgenus rank the new genera arising from genus splits considered to be unwarranted. According to the Prokaryotic Code, the species in question would be designated with their previous generic synonym and, in parentheses, the subgenus name (which would correspond to the latest synonym used by the databases). Being the subgenus an optional taxonomic category, it can be omitted, but its use may facilitate the mapping of the synonyms in databases and the literature. For illustration, we apply the strategy to recent genus splits in the Mycobacteriales, specifically the new nested genus Prescottella within the rhodococcal radiation and the several new genera into which Mycobacterium was subdivided. Competing Interest Statement The authors have declared no competing interest. Abbreviations - AAI - average amino acids identity - AF - aligned fraction of orthologous genes - ANI - average nucleotide identity - DDBJ - DNA Data Bank of Japan - EMBL-EBI - European Molecular Biology Laboratory-European Bioinformatics Institute - ENA - European Nucleotide Archive - GTR - General Time-Reversible with empirical base frequencies - ICNP - International Code of Nomenclature of Prokaryotes - ICSP - International Committee on Systematics of Prokaryotes - INSDC - International Nucleotide Sequence Database Collaboration - LPSN - Lists of Prokaryotic names with Standing in Nomenclature (https://www.bacterio.net - Mbp - mega base pairs - ML - maximum likelihood - MLD - maximum likelihood distance - NCBI - National Center for Biotechnology Information - PAM - “Patogénesis Microbiana” isolate collection of Vazquez-Boland’s laboratory - POCP - percentage of conserved proteins - RED - relative evolutionary distance - TaxID - taxonomy identified - WGS - whole genome sequencing - +ASC - ascertainment bias correction - +F - empirical base frequencies - +R - FreeRate model categories.