of M. kansasii. The strains belonging to subtype 2 are circumscribed by the type strain of M. persicum, a recently described
species. The remaining strains are not circumscribed by any type
strains in the analysis, represent species-level lineages, and were
elevated to novel independent species. The strains belonging to
subtype 3 are the most closely related to M. kansasii and are
reclassified as M. pseudokansasii. The strains belonging to subtype
5 are reclassified as M. innocens, and the strains belonging to
subtype 6 are reclassified as M. attenuatum [104].
Finally, the most recent major change is also probably the most
controversial, namely, the taxonomic division of the genus Mycobacterium into five different genera: Mycobacterium, Mycolicibacter,
Mycolicibacillus, Mycolicibacterium, and Mycobacteroides [12]. The
authors used 1941 core protein sequences from the WGS of
150 mycobacterial type strains to identify conserved signature
indels (CSIs) that illustrated five distinct phylogenetic clades.
These clades were proposed as the aforementioned four novel
genera and an emended Mycobacterium genus. This major reclassification generated significant controversy among some
mycobacteriologists [13].
Although this reclassification was validly published and thus is
considered official, the taxonomic classifications of prokaryotic taxa
remain taxonomic opinions. As correctly stated by Tortoli, et al.
[13], researchers have the freedom to use the nomenclatural designations that best align with their taxonomic opinions. Not only is
there no mechanism to enforce the use of particular nomenclature
over another (with the very limited and infrequently used exception
of nomina rejicienda, i.e., rejected names), doing so would contravene one of the core principles of the International Code of
Nomenclature of Prokaryotes: “Nothing in this Code may be
construed to restrict the freedom of taxonomic thought or action”
[103]. In general, the scientific community tends to accept reclassifications at the species and subspecies levels, which have clearer
definitions and circumscription limits. However, when a reclassification affects the level of genus or above, the definition is less clear,
making it difficult to obtain a scientific consensus on the “proper”
nomenclature to use. This division of the Mycobacterium genus
represents such an example and remains controversial.
WGS-based techniques such as dDDH and ANI have shown
great usefulness in elucidating the phylogenomic relationships of
bacterial organisms. This has allowed us to properly classify many
mycobacterial species, both by consolidating genomically similar
species that were previously regarded as different species and by
recognition of genomically distinct strains as independent species.
Mycobacterial ID and Characterization Using WGS
433
species. The remaining strains are not circumscribed by any type
strains in the analysis, represent species-level lineages, and were
elevated to novel independent species. The strains belonging to
subtype 3 are the most closely related to M. kansasii and are
reclassified as M. pseudokansasii. The strains belonging to subtype
5 are reclassified as M. innocens, and the strains belonging to
subtype 6 are reclassified as M. attenuatum [104].
Finally, the most recent major change is also probably the most
controversial, namely, the taxonomic division of the genus Mycobacterium into five different genera: Mycobacterium, Mycolicibacter,
Mycolicibacillus, Mycolicibacterium, and Mycobacteroides [12]. The
authors used 1941 core protein sequences from the WGS of
150 mycobacterial type strains to identify conserved signature
indels (CSIs) that illustrated five distinct phylogenetic clades.
These clades were proposed as the aforementioned four novel
genera and an emended Mycobacterium genus. This major reclassification generated significant controversy among some
mycobacteriologists [13].
Although this reclassification was validly published and thus is
considered official, the taxonomic classifications of prokaryotic taxa
remain taxonomic opinions. As correctly stated by Tortoli, et al.
[13], researchers have the freedom to use the nomenclatural designations that best align with their taxonomic opinions. Not only is
there no mechanism to enforce the use of particular nomenclature
over another (with the very limited and infrequently used exception
of nomina rejicienda, i.e., rejected names), doing so would contravene one of the core principles of the International Code of
Nomenclature of Prokaryotes: “Nothing in this Code may be
construed to restrict the freedom of taxonomic thought or action”
[103]. In general, the scientific community tends to accept reclassifications at the species and subspecies levels, which have clearer
definitions and circumscription limits. However, when a reclassification affects the level of genus or above, the definition is less clear,
making it difficult to obtain a scientific consensus on the “proper”
nomenclature to use. This division of the Mycobacterium genus
represents such an example and remains controversial.
WGS-based techniques such as dDDH and ANI have shown
great usefulness in elucidating the phylogenomic relationships of
bacterial organisms. This has allowed us to properly classify many
mycobacterial species, both by consolidating genomically similar
species that were previously regarded as different species and by
recognition of genomically distinct strains as independent species.
Mycobacterial ID and Characterization Using WGS
433