Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium

• Published in: Infection, genetics and evolution genetics and evolution, 2019-11, Vol.75, p.103983-103983, Article 103983
• Main Authors: Tortoli, Enrico, Meehan, Conor J., Grottola, Antonella, Fregni Serpini, Giulia, Fabio, Anna, Trovato, Alberto, Pecorari, Monica, Cirillo, Daniela M.
• Format: Article
• Language: English
• Subjects: Average nucleotide identity; DNA Barcoding, Taxonomic - methods; Genome to genome distance; Genome, Bacterial; Mycobacterium; Mycobacterium - classification; Mycobacterium - genetics; Phylogeny; Sequence Analysis, DNA; Synonymous taxa; Taxonomy
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2019.103983

The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and “M. avium subsp. hominissuis”), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections. •All the Mycobacterium species with available genome have been investigated.•Average Nucleotide Identity and Genome to genome distance were used for comparison.•A number of synonymous species were detected and a revision of the taxonomy was proposed.