The species of the Mycobacterium tuberculosis Complex
(MTBC) include M. tuberculosis, M. africanum, M. bovis,
M. caprae, M. microti, and M. pinnipedii, as well as several taxa
that have not been validly published according to the International
Code of Nomenclature of Prokaryotes [103]. However, when the
type strains are compared against M. tuberculosis H37Rv
T using
both dDDH and ANI, it is abundantly clear that all of these
“species” fall well within the genomic circumscription of
M. tuberculosis. Pairwise dDDH values range from 91.2% to
99.2% (significantly above the 70% threshold), while pairwise ANI
values range from 99.21% to 99.92% (significantly above the
95–96% threshold). Thus, these all represent strains of the same
species, namely, M. tuberculosis, as it has nomenclatural priority over
the other names, i.e., they are later heterotypic synonyms of
M. tuberculosis. Although these taxa may display differential phenotypic or genomic characteristics (e.g., morphologies, SNPs, and
spoligotypes) that allow differentiation into coherent lineages that
in some cases mirror the previous species designations, the global
genomic similarity between all these taxa suggests that all the
“species” of the MTBC might be more accurately considered variants of M. tuberculosis that likely represent host-adapted ecotypes.
In order to retain the conceptual grouping of these taxa despite
their reclassification as M. tuberculosis, it has been recommended
that the previous specific epithet be incorporated as an infrasubspecific designation, e.g., M. tuberculosis variant bovis [17].
Also, using both dDDH and ANI, Tortoli et al. determined
that numerous taxa within Mycobacterium represent synonymous
taxa, some of which are described here. M. chelonae subsp. gwanakae was found to be a later heterotypic synonym of M. chelonae
subsp. bovis. M. fortuitum subsp. acetamidolyticum was found to be
a later heterotypic synonym of M. fortuitum subsp. fortuitum; their
consolidation into a single taxon would effectively eliminate any
subspecies, leaving simply M. fortuitum. M. avium subsp. paratuberculosis, M. avium subsp. silvaticum, and “M. avium subsp.
hominissuis” were found to be later heterotypic synonyms of
M. avium subsp. avium. Additionally, M. lepraemurium was
found to be circumscribed by M. avium but distant enough to
represent a new subspecies, M. avium subsp. lepraemurium.
M. paraintracellulare was found to be a later heterotypic synonym
of M. intracellulare subsp. intracellulare, and M. intracellulare
subsp. yongonense was found to be a later heterotypic synonym of
M. intracellulare subsp. chimaera [11]. Most of these names, however, have not been validly published according to the nomenclatural rules [103] and are therefore unofficial.
A similar study used the same techniques to examine the phylogenomic relationships between the five M. kansasii subtypes. The
strains belonging to subtype 1 are circumscribed by the type strain
432
Marco A. Riojas et al.
(MTBC) include M. tuberculosis, M. africanum, M. bovis,
M. caprae, M. microti, and M. pinnipedii, as well as several taxa
that have not been validly published according to the International
Code of Nomenclature of Prokaryotes [103]. However, when the
type strains are compared against M. tuberculosis H37Rv
T using
both dDDH and ANI, it is abundantly clear that all of these
“species” fall well within the genomic circumscription of
M. tuberculosis. Pairwise dDDH values range from 91.2% to
99.2% (significantly above the 70% threshold), while pairwise ANI
values range from 99.21% to 99.92% (significantly above the
95–96% threshold). Thus, these all represent strains of the same
species, namely, M. tuberculosis, as it has nomenclatural priority over
the other names, i.e., they are later heterotypic synonyms of
M. tuberculosis. Although these taxa may display differential phenotypic or genomic characteristics (e.g., morphologies, SNPs, and
spoligotypes) that allow differentiation into coherent lineages that
in some cases mirror the previous species designations, the global
genomic similarity between all these taxa suggests that all the
“species” of the MTBC might be more accurately considered variants of M. tuberculosis that likely represent host-adapted ecotypes.
In order to retain the conceptual grouping of these taxa despite
their reclassification as M. tuberculosis, it has been recommended
that the previous specific epithet be incorporated as an infrasubspecific designation, e.g., M. tuberculosis variant bovis [17].
Also, using both dDDH and ANI, Tortoli et al. determined
that numerous taxa within Mycobacterium represent synonymous
taxa, some of which are described here. M. chelonae subsp. gwanakae was found to be a later heterotypic synonym of M. chelonae
subsp. bovis. M. fortuitum subsp. acetamidolyticum was found to be
a later heterotypic synonym of M. fortuitum subsp. fortuitum; their
consolidation into a single taxon would effectively eliminate any
subspecies, leaving simply M. fortuitum. M. avium subsp. paratuberculosis, M. avium subsp. silvaticum, and “M. avium subsp.
hominissuis” were found to be later heterotypic synonyms of
M. avium subsp. avium. Additionally, M. lepraemurium was
found to be circumscribed by M. avium but distant enough to
represent a new subspecies, M. avium subsp. lepraemurium.
M. paraintracellulare was found to be a later heterotypic synonym
of M. intracellulare subsp. intracellulare, and M. intracellulare
subsp. yongonense was found to be a later heterotypic synonym of
M. intracellulare subsp. chimaera [11]. Most of these names, however, have not been validly published according to the nomenclatural rules [103] and are therefore unofficial.
A similar study used the same techniques to examine the phylogenomic relationships between the five M. kansasii subtypes. The
strains belonging to subtype 1 are circumscribed by the type strain
432
Marco A. Riojas et al.