@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@book{Hauduroy1955a,
  author = {Hauduroy, P.},
  year = {1955},
  title = {Derniers aspects du monde des mycobactéries},
  publisher = {Masson et Cie},
  address = {Paris}
}


@article{KarlsonLessel1970a,
  year = {1970},
  journal = {International Journal of Systematic Bacteriology},
  volume = {20},
  pages = {273-282},
  author = {Karlson, A.G. and Lessel, E.F.},
  title = {\textit{Mycobacterium bovis} nom. nov.},
  doi = {10.1099/00207713-20-3-273},
  issue = {3}
}

@article{NiemannEtAl2002a,
  year = {2002},
  journal = {Int J Syst Evol Microbiol},
  volume = {52},
  pages = {433-436},
  author = {Niemann, S. and Richter, E. and Rusch-Gerdes, S.},
  title = {Biochemical and genetic evidence for the transfer of \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} Aranaz et al. 1999 to the species \textit{Mycobacterium bovis} Karlson and Lessel 1970 (approved lists 1980) as \textit{Mycobacterium bovis} subsp. \textit{caprae} comb. nov.},
  abstract = {We propose to replace the species designation \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} (Aranaz et al. 1999) by \textit{Mycobacterium bovis} subsp. \textit{caprae} comb. nov., since isolates of this subspecies share their main growth, biochemical and genetic characteristics with \textit{M. bovis} and not with \textit{M. tuberculosis}. These include negative biochemical test results for niacin accumulation and nitrate reduction as well as genetic features like the presence of an \textit{M. bovis}-specific mutation in the oxyR locus, absence of the mtp40 sequence and a specific mutation in the gyrB gene, all of which have been described as characteristics for the differentiation of \textit{M. bovis}. The only obvious biochemical character that differentiates the caprae subtype from other \textit{M. bovis} isolates is susceptibility to pyrazinamide (PZA), which is due to the lack of a single point mutation in the pncA gene. However, susceptibility to PZA among clinical isolates of \textit{M. bovis} isolates has been reported previously and, thus, may now been explained by a PZA-susceptible subspecies of \textit{M. bovis}. We conclude that the species designation \textit{M. tuberculosis} subsp. \textit{caprae} is misleading and not correct in light of the biochemical and genetic characteristics and propose that the accurate designation of isolates of this subtype is \textit{M. bovis} subsp. \textit{caprae}.},
  doi = {10.1099/00207713-52-2-433},
  issue = {2},
  pmid = {11931153}
}


@article{CastetsEtAl1969a,
  year = {1969},
  journal = {Médecine d'Afrique Noire},
  volume = {16},
  pages = {321-322},
  author = {Castets, M. and Rist, N. and Boisvert, H.},
  title = {La variété africaine du bacille tuberculeux humain.}
}


@article{CousinsEtAl2003a,
  year = {2003},
  journal = {Int J Syst Evol Microbiol},
  volume = {53},
  pages = {1305-1314},
  author = {Cousins, D.V. and Bastida, R. and Cataldi, A. and Quse, V. and Redrobe, S. and Dow, S. and Duignan, P. and Murray, A. and Dupont, C. and Ahmed, N. and Collins, D.M. and Butler, W.R. and Dawson, D. and Rodriguez, D. and Loureiro, J. and Romano, M.I. and Alito, A. and Zumarraga, M. and Bernardelli, A.},
  title = {Tuberculosis in seals caused by a novel member of the \textit{Mycobacterium tuberculosis} complex: \textit{Mycobacterium pinnipedii} sp. nov.},
  abstract = {A comparison of \textit{Mycobacterium tuberculosis} complex isolates from seals (pinnipeds) in Australia, Argentina, Uruguay, Great Britain and New Zealand was undertaken to determine their relationships to each other and their taxonomic position within the complex. Isolates from 30 cases of tuberculosis in six species of pinniped and seven related isolates were compared to representative and standard strains of the \textit{M. tuberculosis} complex. The seal isolates could be distinguished from other members of the \textit{M. tuberculosis} complex, including the recently defined '\textit{Mycobacterium canettii}' and '\textit{Mycobacterium caprae}', on the basis of host preference and phenotypic and genetic tests. Pinnipeds appear to be the natural host for this 'seal bacillus', although the organism is also pathogenic in guinea pigs, rabbits, humans, Brazilian tapir (Tapirus terrestris) and, possibly, cattle. Infection caused by the seal bacillus is predominantly associated with granulomatous lesions in the peripheral lymph nodes, lungs, pleura, spleen and peritoneum. Cases of disseminated disease have been found. As with other members of the \textit{M. tuberculosis} complex, aerosols are the most likely route of transmission. The name \textit{Mycobacterium pinnipedii} sp. nov. is proposed for this novel member of the \textit{M. tuberculosis} complex (the type strain is 6482\textsuperscript{T}=ATCC BAA-688\textsuperscript{T}=NCTC 13288\textsuperscript{T}).},
  doi = {10.1099/ijs.0.02401-0},
  issue = {5},
  pmid = {13130011}
}


@article{Aronson1926a,
  year = {1926},
  journal = {Journal of Infectious Diseases},
  volume = {39},
  pages = {314-320},
  author = {Aronson, J.D.},
  title = {Spontaneous tuberculosis in salt water fish.},
  doi = {10.1093/infdis/39.4.315}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{TsukamuraEtAl1981a,
  year = {1981},
  journal = {Int. J. Syst. Bacteriol.},
  volume = {31},
  pages = {263-275},
  author = {Tsukamura, M. and Mizuno, S. and Tsukamura, S.},
  title = {Numerical analysis of rapidly growing, scotochromogenic mycobacteria, including \textit{Mycobacterium obuense} sp. nov., nom. rev., \textit{Mycobacterium rhodesiae} sp. nov., nom. rev., \textit{Mycobacterium aichiense} sp. nov., nom. rev., \textit{Mycobacterium chubuense} sp. nov., nom. rev., and \textit{Mycobacterium tokaiense} sp. nov., nom. rev.},
  doi = {10.1099/00207713-31-3-263},
  issue = {3}
}


@article{TaginiEtAl2019a,
  year = {2019},
  journal = {Int J Syst Evol Microbiol},
  volume = {69},
  pages = {1696-1704},
  author = {Tagini, F. and Aeby, S. and Bertelli, C. and Droz, S. and Casanova, C. and Prod'hom, G. and Jaton, K. and Greub, G.},
  title = {Phylogenomics reveal that \textit{Mycobacterium kansasii} subtypes are species-level lineages. Description of \textit{Mycobacterium pseudokansasii} sp. nov., \textit{Mycobacterium innocens} sp. nov. and \textit{Mycobacterium attenuatum} sp. nov.},
  abstract = {Among the species \textit{Mycobacterium kansasii}, seven subtypes have been previously reported based on the PCR and the restriction fragment length polymorphism of the gene hsp65. Here, we used whole-genome sequencing to refine \textit{M. kansasii} taxonomy and correct multiple inconsistencies. Average nucleotide identity (ANI) values between \textit{M. kansasii} subtypes ranged from 88.4 to 94.2 %, lower than the accepted 95-96 % cut-off for species delineation. In addition, \textit{Mycobacterium gastri} was closer to the \textit{M. kansasii} subtypes 1, 2, 3, 4 and 5 than \textit{M. kansasii} subtype 6. The recently described species \textit{Mycobacterium persicum} shared 99.77 % ANI with \textit{M. kansasii} subtype 2. Consistent with the ANI results, the digital DNA-DNA hybridization value was below the 70 % threshold for species delineation between subtypes and above it within subtypes as well as between subtype 2 and \textit{M. persicum}. Furthermore, core-genome phylogeny confirmed the current \textit{M. kansasii} species to be polyphyletic. Hence, we propose (i) \textit{Mycobacterium pseudokansasii} sp. nov., replacing subtype 3, with the type strain MK142\textsuperscript{T}(=CCUG 72128\textsuperscript{T}=DSM 107152\textsuperscript{T}), (ii) \textit{Mycobacterium innocens} sp. nov., replacing subtype 5, with the type strain MK13\textsuperscript{T} (=CCUG 72126\textsuperscript{T}=DSM 107161\textsuperscript{T}), and (iii) \textit{Mycobacterium attenuatum} sp. nov., replacing subtype 6, with the type strain MK41\textsuperscript{T}(=CCUG 72127\textsuperscript{T}=DSM 107153\textsuperscript{T}). Subtype 4 represents a new species-level lineage based on the genomic data but no strain was available. No genome sequence or strain was available for subtype 7. The proposed nomenclature will facilitate the identification of the most pathogenic subtype 1 as \textit{M. kansasii} by clinicians while the new species names suggest the attenuated pathogenicity of the other subtypes.},
  doi = {10.1099/ijsem.0.003378},
  issue = {6},
  pmid = {30950782}
}


@article{CastejonEtAl2018a,
  year = {2018},
  journal = {Int J Syst Evol Microbiol},
  volume = {68},
  pages = {1998-2005},
  author = {Castejon, M. and Menendez, M.C. and Comas, I. and Vicente, A. and Garcia, M.J.},
  title = {Whole-genome sequence analysis of the \textit{Mycobacterium avium} complex and proposal of the transfer of \textit{Mycobacterium yongonense} to \textit{Mycobacterium intracellulare} subsp. \textit{yongonense} subsp. nov.},
  abstract = {Bacterial whole-genome sequences contain informative features of their evolutionary pathways. Comparison of whole-genome sequences have become the method of choice for classification of prokaryotes, thus allowing the identification of bacteria from an evolutionary perspective, and providing data to resolve some current controversies. Currently, controversy exists about the assignment of members of the \textit{Mycobacterium avium} complex, as is for the cases of \textit{Mycobacterium yongonense} and '\textit{Mycobacterium} indicus pranii'. These two mycobacteria, closely related to \textit{Mycobacterium intracellulare} on the basis of standard phenotypic and single gene-sequences comparisons, were not considered a member of such species on the basis on some particular differences displayed by a single strain. Whole-genome sequence comparison procedures, namely the average nucleotide identity and the genome distance, showed that those two mycobacteria should be considered members of the species \textit{M. intracellulare}. The results were confirmed with other whole-genome comparison supplementary methods. According to the data provided, \textit{Mycobacterium yongonense} and '\textit{Mycobacterium} indicus pranii' should be considered and renamed and included as members of \textit{M. intracellulare}. This study highlights the problems caused when a novel species is accepted on the basis of a single strain, as was the case for \textit{M. yongonense}. Based mainly on whole-genome sequence analysis, we conclude that \textit{M. yongonense} should be reclassified as a subspecies of \textit{Mycobacterium} intracellulareas \textit{Mycobacterium} intracellularesubsp. yongonense and '\textit{Mycobacterium} indicus pranii' classified in the same subspecies as the type strain of \textit{Mycobacterium intracellulare} and classified as \textit{Mycobacterium} intracellularesubsp. intracellulare.},
  doi = {10.1099/ijsem.0.002767},
  issue = {6},
  pmid = {29683417}
}

@article{CuttinoMccabe1949b,
  year = {1949},
  journal = {American Journal of Clinical Pathology},
  volume = {25},
  pages = {1-34},
  author = {Cuttino, J.T. and McCabe, A.M.},
  title = {Pure granulomatous nocardiosis: A new fungus disease distinguished by intracellular parasitism.}
}

@article{Runyon1965a,
  year = {1965},
  journal = {Advances in Tuberculosis Research},
  volume = {14},
  pages = {235-287},
  author = {Runyon, E.H.},
  title = {Pathogenic mycobacteria.}
}


@article{AranazEtAl1999a,
  year = {1999},
  journal = {Int J Syst Bacteriol},
  volume = {49},
  pages = {1263-1273},
  author = {Aranaz, A. and Liebana, E. and Gomez-Mampaso, E. and Galan, J.C. and Cousins, D. and Ortega, A. and Blazquez, J. and Baquero, F. and Mateos, A. and Suarez, G. and Dominguez, L.},
  title = {\textit{Mycobacterium tuberculosis} subsp. \textit{caprae} subsp. nov.: a taxonomic study of a new member of the \textit{Mycobacterium tuberculosis} complex isolated from goats in Spain.},
  abstract = {Isolates from the \textit{Mycobacterium tuberculosis} complex cultured from caprine pathological tissue samples were biochemically and genetically characterized. The isolates were negative for nitrate reduction and niacin accumulation, they weakly hydrolysed Tween 80, were sensitive to pyrazinamide (50 micrograms ml-1) and were resistant to 1 and 2 micrograms tiophene-2-carboxylic acid hydrazide ml-1 but not to 5 or 10 micrograms tiophene-2-carboxylic acid hydrazide ml-1. Sequencing of the pncA gene revealed a polymorphism characteristic of \textit{M. tuberculosis}, whereas oxyR, katG and gyrA sequences were characteristic of \textit{Mycobacterium bovis}. The fingerprinting patterns obtained with IS6110, direct repeats and polymorphic G+C-rich sequence-associated RFLP and direct variable repeat-spacer oligonucelotide typing (spoligotyping) segregated these isolates from the other members of the complex. The results of this testing, together with the repeated association of this micro-organism with goats, suggest that a new member of this taxonomic complex not matching any of the classical species had been identified. This unusual mycobacterium may play a role in the epidemiology of animal and human tuberculosis in Spain. The name \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} subsp. nov. is proposed for these isolates. The type strain of \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} subsp. nov. is gM-1T (= CIP 105776T).},
  doi = {10.1099/00207713-49-3-1263},
  issue = {3},
  pmid = {10425790}
}

@article{RiojasEtAl2018a,
  year = {2018},
  journal = {Int J Syst Evol Microbiol},
  volume = {68},
  pages = {324-332},
  author = {Riojas, M.A. and McGough, K.J. and Rider-Riojas, C.J. and Rastogi, N. and Hazbon, M.H.},
  title = {Phylogenomic analysis of the species of the \textit{Mycobacterium tuberculosis} complex demonstrates that \textit{Mycobacterium africanum}, \textit{Mycobacterium bovis}, \textit{Mycobacterium caprae}, \textit{Mycobacterium microti} and \textit{Mycobacterium pinnipedii} are later heterotypic synonyms of \textit{Mycobacterium tuberculosis}.},
  abstract = {The species within the \textit{Mycobacterium tuberculosis} Complex (MTBC) have undergone numerous taxonomic and nomenclatural changes, leaving the true structure of the MTBC in doubt. We used next-generation sequencing (NGS), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) to investigate the relationship between these species. The type strains of \textit{Mycobacterium africanum}, \textit{Mycobacterium bovis}, \textit{Mycobacterium caprae}, \textit{Mycobacterium microti} and \textit{Mycobacterium pinnipedii} were sequenced via NGS. Pairwise dDDH and ANI comparisons between these, previously sequenced MTBC type strain genomes (including '\textit{Mycobacterium canettii}', '\textit{Mycobacterium mungi}' and '\textit{Mycobacterium orygis}') and \textit{M. tuberculosis} H37Rv\textsuperscript{T} were performed. Further, all available genome sequences in GenBank for species in or putatively in the MTBC were compared to H37Rv\textsuperscript{T}. Pairwise results indicated that all of the type strains of the species are extremely closely related to each other (dDDH: 91.2-99.2 %, ANI: 99.21-99.92 %), greatly exceeding the respective species delineation thresholds, thus indicating that they belong to the same species. Results from the GenBank genomes indicate that all the strains examined are within the circumscription of H37Rv\textsuperscript{T} (dDDH: 83.5-100 %). We, therefore, formally propose a union of the species of the MTBC as \textit{M. tuberculosis}. \textit{M. africanum}, \textit{M. bovis}, \textit{M. caprae}, \textit{M. microti} and \textit{M. pinnipedii} are reclassified as later heterotypic synonyms of \textit{M. tuberculosis}. '\textit{M. canettii}', '\textit{M. mungi}', and '\textit{M. orygis}' are classified as strains of the species \textit{M. tuberculosis}. We further recommend use of the infrasubspecific term 'variant' ('var.') and infrasubspecific designations that generally retain the historical nomenclature associated with the groups or otherwise convey such characteristics, e.g. \textit{M. tuberculosis} var. bovis.},
  doi = {10.1099/ijsem.0.002507},
  issue = {1},
  pmid = {29205127}
}

@book{LehmannNeumann1896a,
  author = {Lehmann, K.B. and Neumann, R.},
  year = {1896},
  title = {Atlas und Grundriss der Bakteriologie und Lehrbuch der speziellen bakteriologischen Diagnostik, 1st ed.},
  publisher = {J.F. Lehmann},
  address = {München}
}

@book{Zopf1883a,
  author = {Zopf, W.},
  year = {1883},
  title = {Die Spaltpilze},
  publisher = {Edward Trewendt},
  address = {Breslau}
}


@article{FogelsonEtAl2018a,
  year = {2018},
  journal = {Int J Syst Evol Microbiol},
  volume = {68},
  pages = {3696-3700},
  author = {Fogelson, S.B. and Camus, A.C. and Lorenz, W. and Phillips, A. and Bartlett, P. and Sanchez, S.},
  title = {\textit{Mycobacterium syngnathidarum} sp. nov., a rapidly growing mycobacterium identified in syngnathid fish.},
  abstract = {Two closely related isolates, 27335\textsuperscript{T} and 24999, of rapidly growing, non-pigmented mycobacteria, were cultured from two clinically ill fish of the family Syngnathidae. Whole genome sequencing of the two isolates revealed low sequence homology to documented mycobacteria within public databases such as the NCBI. Evaluation of targeted housekeeping genes, including 16S rRNA, ITS, rpoB and hsp65, related the two bacteria distantly to \textit{Mycobacterium senegalense} CK2 M4421 and \textit{Mycobacterium farcinogenes} DSM 43637. Phenotypic, biochemical and dDNA-DNA hybridization tests demonstrated that \textit{Mycobacterium syngnathidarum} is a new species distinct from other recognized rapidly growing mycobacterial species. Phenotypic, chemotaxonomic and phylogenetic data evaluation provided evidence that the two strains represent one novel species. We propose the formal recognition of \textit{Mycobacterium syngnathidarum} sp. nov., with isolate 27335\textsuperscript{T} as the type strain (=ATCC TSD-89\textsuperscript{T},=DSM 105112\textsuperscript{T}).},
  doi = {10.1099/ijsem.0.002978},
  issue = {12},
  pmid = {30272539}
}


@article{TaginiEtAl2019a,
  year = {2019},
  journal = {Int J Syst Evol Microbiol},
  volume = {69},
  pages = {1696-1704},
  author = {Tagini, F. and Aeby, S. and Bertelli, C. and Droz, S. and Casanova, C. and Prod'hom, G. and Jaton, K. and Greub, G.},
  title = {Phylogenomics reveal that \textit{Mycobacterium kansasii} subtypes are species-level lineages. Description of \textit{Mycobacterium pseudokansasii} sp. nov., \textit{Mycobacterium innocens} sp. nov. and \textit{Mycobacterium attenuatum} sp. nov.},
  abstract = {Among the species \textit{Mycobacterium kansasii}, seven subtypes have been previously reported based on the PCR and the restriction fragment length polymorphism of the gene hsp65. Here, we used whole-genome sequencing to refine \textit{M. kansasii} taxonomy and correct multiple inconsistencies. Average nucleotide identity (ANI) values between \textit{M. kansasii} subtypes ranged from 88.4 to 94.2 %, lower than the accepted 95-96 % cut-off for species delineation. In addition, \textit{Mycobacterium gastri} was closer to the \textit{M. kansasii} subtypes 1, 2, 3, 4 and 5 than \textit{M. kansasii} subtype 6. The recently described species \textit{Mycobacterium persicum} shared 99.77 % ANI with \textit{M. kansasii} subtype 2. Consistent with the ANI results, the digital DNA-DNA hybridization value was below the 70 % threshold for species delineation between subtypes and above it within subtypes as well as between subtype 2 and \textit{M. persicum}. Furthermore, core-genome phylogeny confirmed the current \textit{M. kansasii} species to be polyphyletic. Hence, we propose (i) \textit{Mycobacterium pseudokansasii} sp. nov., replacing subtype 3, with the type strain MK142\textsuperscript{T}(=CCUG 72128\textsuperscript{T}=DSM 107152\textsuperscript{T}), (ii) \textit{Mycobacterium innocens} sp. nov., replacing subtype 5, with the type strain MK13\textsuperscript{T} (=CCUG 72126\textsuperscript{T}=DSM 107161\textsuperscript{T}), and (iii) \textit{Mycobacterium attenuatum} sp. nov., replacing subtype 6, with the type strain MK41\textsuperscript{T}(=CCUG 72127\textsuperscript{T}=DSM 107153\textsuperscript{T}). Subtype 4 represents a new species-level lineage based on the genomic data but no strain was available. No genome sequence or strain was available for subtype 7. The proposed nomenclature will facilitate the identification of the most pathogenic subtype 1 as \textit{M. kansasii} by clinicians while the new species names suggest the attenuated pathogenicity of the other subtypes.},
  doi = {10.1099/ijsem.0.003378},
  issue = {6},
  pmid = {30950782}
}


@article{Dacostacruz1938a,
  year = {1938},
  journal = {Acta Medica (Rio de Janeiro)},
  volume = {1},
  pages = {297-301},
  author = {Da Costa Cruz, J.C.},
  title = {\textit{Mycobacterium fortuitum} um novo bacillo acidoresistance pathogenico para o homen.}
}

@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{TsukamuraEtAl1986a,
  year = {1986},
  journal = {Microbiol Immunol},
  volume = {30},
  pages = {97-110},
  author = {Tsukamura, M. and Yano, I. and Imaeda, T.},
  title = {\textit{Mycobacterium fortuitum} subspecies acetamidolyticum, a new subspecies of \textit{Mycobacterium fortuitum}.},
  abstract = {\textit{Mycobacterium fortuitum} subspecies acetamidolyticum is a new subspecies of \textit{M. fortuitum} and has an intermediate growth rate. It is a nonphotochromogenic mycobacterium. It does not utilize glutamate but utilizes acetamide as a simultaneous nitrogen and carbon source. It is able to utilize acetate, malate, pyruvate, fumarate, glucose, fructose, and n-propanol as the sole sources of carbon in the presence of ammoniacal nitrogen, but does not utilize them in the presence of glutamate-nitrogen. It is easily differentiated from all rapidly growing mycobacteria by its inability to utilize glutamate as a simultaneous nitrogen and carbon source, and from all slowly growing mycobacteria by its capacity to utilize acetamide as a simultaneous nitrogen and carbon source. Its mycolic acid pattern is different from that of \textit{M. fortuitum}. However, its deoxyribonucleic acid showed 94% relatedness with that of \textit{M. fortuitum}. In view of the above findings, it has been designated as a new subspecies of \textit{M. fortuitum}. The organism was isolated from sputum of a 56-year-old patient with lung disease and is considered to be a lung pathogen. The type strain is ATCC 35931 (NCH E11620).},
  doi = {10.1111/j.1348-0421.1986.tb00925.x},
  issue = {2},
  pmid = {3713561}
}


@article{SethsmithEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {3184},
  author = {Seth-Smith, H.M.B. and Imkamp, F. and Tagini, F. and Cuenod, A. and Homke, R. and Jahn, K. and Tschacher, A. and Grendelmeier, P. and Battig, V. and Erb, S. and Reinhard, M. and Rutimann, G. and Borrell, S. and Gagneux, S. and Casanova, C. and Droz, S. and Osthoff, M. and Tamm, M. and Nubel, U. and Greub, G. and Keller, P.M. and Egli, A.},
  title = {Discovery and Characterization of \textit{Mycobacterium basiliense} sp. nov., a Nontuberculous \textit{Mycobacterium} Isolated From Human Lungs.},
  abstract = {\textit{Bacteria} belonging to the genus \textit{Mycobacterium} are predominantly responsible for pulmonary diseases; most notably \textit{Mycobacterium tuberculosis} causes granulomatous pulmonary infections. Here we describe a novel slow growing mycobacterial species isolated from respiratory samples from five patients, four with underlying pulmonary disease. The isolates were characterized by biochemical and molecular techniques, including whole genome sequencing. Biochemical characteristics generally match those of \textit{M. marinum} and \textit{M. ulcerans}; however, the most striking difference of the new species is its ability to grow at 37 degrees C. The new species was found to grow in human macrophages, but not amoebae, suggesting a pathogenic rather than an environmental lifestyle. Phylogenetic analysis reveals a deep-rooting relationship to \textit{M. marinum} and \textit{M. ulcerans}. A complete genome sequence was obtained through combining short and long-read sequencing, providing a genome of 5.6 Mb. The genome appears to be highly intact, syntenic with that of \textit{M. marinum}, with very few insertion sequences. A vast array of virulence factors includes 283 PE/PPE surface-associated proteins, making up 10% of the coding capacity, and 22 non-ribosomal peptide synthase clusters. A comparison of six clinical isolates from the five patients shows that they differ by up to two single nucleotide polymorphisms, suggesting a common source of infection. Our findings are in accordance with the recognition of a new taxonomic entity. We propose the name \textit{M. basiliense}, as all isolates were found in patients from the Basel area of Switzerland.},
  doi = {10.3389/fmicb.2018.03184},
  pmid = {30671031}
}


@article{NouiouiEtAl2017h,
  year = {2017},
  journal = {Int J Syst Evol Microbiol},
  volume = {67},
  pages = {4948-4955},
  author = {Nouioui, I. and Sangal, V. and Carro, L. and Teramoto, K. and Jando, M. and Montero-Calasanz, M.D.C. and Igual, J.M. and Sutcliffe, I. and Goodfellow, M. and Klenk, H.P.},
  title = {Two novel species of rapidly growing mycobacteria: \textit{Mycobacterium lehmannii} sp. nov. and \textit{Mycobacterium neumannii} sp. nov.},
  abstract = {Two rapidly growing mycobacteria with identical 16S rRNA gene sequences were the subject of a polyphasic taxonomic study. The strains formed a well-supported subclade in the mycobacterial 16S rRNA gene tree and were most closely associated with the type strain of \textit{Mycobacterium novocastrense}. Single and multilocus sequence analyses based on hsp65, rpoB and 16S rRNA gene sequences showed that strains SN 1900\textsuperscript{T} and SN 1904\textsuperscript{T} are phylogenetically distinct but share several chemotaxonomic and phenotypic features that are are consistent with their classification in the genus \textit{Mycobacterium}. The two strains were distinguished by their different fatty acid and mycolic acid profiles, and by a combination of phenotypic features. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values for strains SN 1900\textsuperscript{T} and SN 1904\textsuperscript{T} were 61.0 % and 94.7 %, respectively; in turn, the corresponding dDDH and ANI values with \textit{M. novocastrense} DSM 44203\textsuperscript{T} were 41.4 % and 42.8 % and 89.3 % and 89.5 %, respectively. These results show that strains SN1900\textsuperscript{T} and SN 1904\textsuperscript{T} form new centres of taxonomic variation within the genus \textit{Mycobacterium}. Consequently, strains SN 1900\textsuperscript{T} (40\textsuperscript{T}=CECT 8763\textsuperscript{T}=DSM 43219\textsuperscript{T}) and SN 1904\textsuperscript{T} (2409\textsuperscript{T}=CECT 8766\textsuperscript{T}=DSM 43532\textsuperscript{T}) are considered to represent novel species, for which the names Mycobacteriumlehmannii sp. nov. and Mycobacteriumneumannii sp. nov. are proposed. A strain designated as 'Mycobacteriumacapulsensis' was shown to be a bona fide member of the putative novel species, \textit{M. lehmannii}.},
  doi = {10.1099/ijsem.0.002350},
  issue = {12},
  pmid = {29058645}
}


@article{NouiouiEtAl2017h,
  year = {2017},
  journal = {Int J Syst Evol Microbiol},
  volume = {67},
  pages = {4948-4955},
  author = {Nouioui, I. and Sangal, V. and Carro, L. and Teramoto, K. and Jando, M. and Montero-Calasanz, M.D.C. and Igual, J.M. and Sutcliffe, I. and Goodfellow, M. and Klenk, H.P.},
  title = {Two novel species of rapidly growing mycobacteria: \textit{Mycobacterium lehmannii} sp. nov. and \textit{Mycobacterium neumannii} sp. nov.},
  abstract = {Two rapidly growing mycobacteria with identical 16S rRNA gene sequences were the subject of a polyphasic taxonomic study. The strains formed a well-supported subclade in the mycobacterial 16S rRNA gene tree and were most closely associated with the type strain of \textit{Mycobacterium novocastrense}. Single and multilocus sequence analyses based on hsp65, rpoB and 16S rRNA gene sequences showed that strains SN 1900\textsuperscript{T} and SN 1904\textsuperscript{T} are phylogenetically distinct but share several chemotaxonomic and phenotypic features that are are consistent with their classification in the genus \textit{Mycobacterium}. The two strains were distinguished by their different fatty acid and mycolic acid profiles, and by a combination of phenotypic features. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values for strains SN 1900\textsuperscript{T} and SN 1904\textsuperscript{T} were 61.0 % and 94.7 %, respectively; in turn, the corresponding dDDH and ANI values with \textit{M. novocastrense} DSM 44203\textsuperscript{T} were 41.4 % and 42.8 % and 89.3 % and 89.5 %, respectively. These results show that strains SN1900\textsuperscript{T} and SN 1904\textsuperscript{T} form new centres of taxonomic variation within the genus \textit{Mycobacterium}. Consequently, strains SN 1900\textsuperscript{T} (40\textsuperscript{T}=CECT 8763\textsuperscript{T}=DSM 43219\textsuperscript{T}) and SN 1904\textsuperscript{T} (2409\textsuperscript{T}=CECT 8766\textsuperscript{T}=DSM 43532\textsuperscript{T}) are considered to represent novel species, for which the names Mycobacteriumlehmannii sp. nov. and Mycobacteriumneumannii sp. nov. are proposed. A strain designated as 'Mycobacteriumacapulsensis' was shown to be a bona fide member of the putative novel species, \textit{M. lehmannii}.},
  doi = {10.1099/ijsem.0.002350},
  issue = {12},
  pmid = {29058645}
}


@article{AranazEtAl1999a,
  year = {1999},
  journal = {Int J Syst Bacteriol},
  volume = {49},
  pages = {1263-1273},
  author = {Aranaz, A. and Liebana, E. and Gomez-Mampaso, E. and Galan, J.C. and Cousins, D. and Ortega, A. and Blazquez, J. and Baquero, F. and Mateos, A. and Suarez, G. and Dominguez, L.},
  title = {\textit{Mycobacterium tuberculosis} subsp. \textit{caprae} subsp. nov.: a taxonomic study of a new member of the \textit{Mycobacterium tuberculosis} complex isolated from goats in Spain.},
  abstract = {Isolates from the \textit{Mycobacterium tuberculosis} complex cultured from caprine pathological tissue samples were biochemically and genetically characterized. The isolates were negative for nitrate reduction and niacin accumulation, they weakly hydrolysed Tween 80, were sensitive to pyrazinamide (50 micrograms ml-1) and were resistant to 1 and 2 micrograms tiophene-2-carboxylic acid hydrazide ml-1 but not to 5 or 10 micrograms tiophene-2-carboxylic acid hydrazide ml-1. Sequencing of the pncA gene revealed a polymorphism characteristic of \textit{M. tuberculosis}, whereas oxyR, katG and gyrA sequences were characteristic of \textit{Mycobacterium bovis}. The fingerprinting patterns obtained with IS6110, direct repeats and polymorphic G+C-rich sequence-associated RFLP and direct variable repeat-spacer oligonucelotide typing (spoligotyping) segregated these isolates from the other members of the complex. The results of this testing, together with the repeated association of this micro-organism with goats, suggest that a new member of this taxonomic complex not matching any of the classical species had been identified. This unusual mycobacterium may play a role in the epidemiology of animal and human tuberculosis in Spain. The name \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} subsp. nov. is proposed for these isolates. The type strain of \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} subsp. nov. is gM-1T (= CIP 105776T).},
  doi = {10.1099/00207713-49-3-1263},
  issue = {3},
  pmid = {10425790}
}

@article{AranazEtAl2003a,
  year = {2003},
  journal = {Int J Syst Evol Microbiol},
  volume = {53},
  pages = {1785-1789},
  author = {Aranaz, A. and Cousins, D. and Mateos, A. and Dominguez, L.},
  title = {Elevation of \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} Aranaz et al. 1999 to species rank as \textit{Mycobacterium caprae} comb. nov., sp. nov.},
  abstract = {\textit{Mycobacterium tuberculosis} complex isolates recovered from goats were originally classified as \textit{Mycobacterium tuberculosis} subsp. \textit{caprae}; however, this subspecies was recently reclassified as \textit{Mycobacterium bovis} subsp. \textit{caprae}. Besides biochemical (sensitivity to pyrazinamide) and epidemiological features, strains of this unusual member of the \textit{M. tuberculosis} complex show a special combination of pncA, oxyR, katG and gyrA gene polymorphisms. Sequence analysis of the gyrB gene in these strains reveals special nucleotide substitutions not found in other members of the \textit{M. tuberculosis} complex that can be used to differentiate caprine mycobacterial strains from \textit{M. bovis} and other members of the \textit{M. tuberculosis} complex. \textit{M. tuberculosis} subsp. \textit{caprae} now appears not to be restricted to Spanish goats, as strains of this organism have been isolated from cattle, wild boar and pigs. Its occurrence has also been reported in France, Austria and Germany. Two studies on the evolution of the \textit{M. tuberculosis} complex based on the presence/absence of regions of difference have shown that the group of caprine isolates (or its ancestor) is older than \textit{M. bovis} (or its ancestor). These findings reinforce the original suggestion that the caprine mycobacterial strains are a taxon of the \textit{M. tuberculosis} complex, independent of \textit{M. bovis}. Within the current context of the existing nomenclature of the \textit{M. tuberculosis} complex, it is proposed that \textit{M. tuberculosis} subsp. \textit{caprae} be elevated to species status, as \textit{Mycobacterium caprae} comb. nov., sp. nov.},
  doi = {10.1099/ijs.0.02532-0},
  issue = {6},
  pmid = {14657105}
}

@article{NiemannEtAl2002a,
  year = {2002},
  journal = {Int J Syst Evol Microbiol},
  volume = {52},
  pages = {433-436},
  author = {Niemann, S. and Richter, E. and Rusch-Gerdes, S.},
  title = {Biochemical and genetic evidence for the transfer of \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} Aranaz et al. 1999 to the species \textit{Mycobacterium bovis} Karlson and Lessel 1970 (approved lists 1980) as \textit{Mycobacterium bovis} subsp. \textit{caprae} comb. nov.},
  abstract = {We propose to replace the species designation \textit{Mycobacterium tuberculosis} subsp. \textit{caprae} (Aranaz et al. 1999) by \textit{Mycobacterium bovis} subsp. \textit{caprae} comb. nov., since isolates of this subspecies share their main growth, biochemical and genetic characteristics with \textit{M. bovis} and not with \textit{M. tuberculosis}. These include negative biochemical test results for niacin accumulation and nitrate reduction as well as genetic features like the presence of an \textit{M. bovis}-specific mutation in the oxyR locus, absence of the mtp40 sequence and a specific mutation in the gyrB gene, all of which have been described as characteristics for the differentiation of \textit{M. bovis}. The only obvious biochemical character that differentiates the caprae subtype from other \textit{M. bovis} isolates is susceptibility to pyrazinamide (PZA), which is due to the lack of a single point mutation in the pncA gene. However, susceptibility to PZA among clinical isolates of \textit{M. bovis} isolates has been reported previously and, thus, may now been explained by a PZA-susceptible subspecies of \textit{M. bovis}. We conclude that the species designation \textit{M. tuberculosis} subsp. \textit{caprae} is misleading and not correct in light of the biochemical and genetic characteristics and propose that the accurate designation of isolates of this subtype is \textit{M. bovis} subsp. \textit{caprae}.},
  doi = {10.1099/00207713-52-2-433},
  issue = {2},
  pmid = {11931153}
}


@incollection{Reed1957a,
  year = {1957},
  booktitle = {Bergey's Manual of Determinative Bacteriology, 7th edition},
  publisher = {The Williams & Wilkins Co},
  address = {Baltimore},
  editor = {Breed, R.S. and Murray, E.G.D. and Smith, N.R.},
  author = {Reed, G.B.},
  title = {Genus \textit{Mycobacterium} (species affecting warm-blooded animals except those causing leprosy),},
  pages = {703-704}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{TsukamuraEtAl1986a,
  year = {1986},
  journal = {Microbiol Immunol},
  volume = {30},
  pages = {97-110},
  author = {Tsukamura, M. and Yano, I. and Imaeda, T.},
  title = {\textit{Mycobacterium fortuitum} subspecies acetamidolyticum, a new subspecies of \textit{Mycobacterium fortuitum}.},
  abstract = {\textit{Mycobacterium fortuitum} subspecies acetamidolyticum is a new subspecies of \textit{M. fortuitum} and has an intermediate growth rate. It is a nonphotochromogenic mycobacterium. It does not utilize glutamate but utilizes acetamide as a simultaneous nitrogen and carbon source. It is able to utilize acetate, malate, pyruvate, fumarate, glucose, fructose, and n-propanol as the sole sources of carbon in the presence of ammoniacal nitrogen, but does not utilize them in the presence of glutamate-nitrogen. It is easily differentiated from all rapidly growing mycobacteria by its inability to utilize glutamate as a simultaneous nitrogen and carbon source, and from all slowly growing mycobacteria by its capacity to utilize acetamide as a simultaneous nitrogen and carbon source. Its mycolic acid pattern is different from that of \textit{M. fortuitum}. However, its deoxyribonucleic acid showed 94% relatedness with that of \textit{M. fortuitum}. In view of the above findings, it has been designated as a new subspecies of \textit{M. fortuitum}. The organism was isolated from sputum of a 56-year-old patient with lung disease and is considered to be a lung pathogen. The type strain is ATCC 35931 (NCH E11620).},
  doi = {10.1111/j.1348-0421.1986.tb00925.x},
  issue = {2},
  pmid = {3713561}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{ShojaeiEtAl1997a,
  year = {1997},
  journal = {Int J Syst Bacteriol},
  volume = {47},
  pages = {1205-1207},
  author = {Shojaei, H. and Goodfellow, M. and Magee, J.G. and Freeman, R. and Gould, F.K. and Brignall, C.G.},
  title = {\textit{Mycobacterium novocastrense} sp. nov., a rapidly growing photochromogenic mycobacterium.},
  abstract = {A strain isolated from a biopsy sample taken from a slowly spreading skin granulation on a child's hand was found to have properties consistent with its classification in the genus \textit{Mycobacterium}. An almost complete gene sequence of the 16S rRNA of the strain was determined following the cloning and sequencing of the amplified gene. The sequence was aligned with those available for mycobacteria, and phylogenetic trees were inferred with four tree-making algorithms. The organism, which formed a distinct phyletic line within the evolutionary radiation occupied by rapidly growing mycobacteria, was readily distinguished from members of validly described species of rapidly growing mycobacteria on the basis of its mycolic acid pattern and a number of other phenotypic features, notably its ability to form yellow pigmented colonies when incubated in the light. The name proposed for this new species is \textit{Mycobacterium novocastrense}. The type strain is DSM 44203.},
  doi = {10.1099/00207713-47-4-1205},
  issue = {4},
  pmid = {9336929}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{StanfordGunthorpe1971a,
  year = {1971},
  journal = {Br J Exp Pathol},
  volume = {52},
  pages = {627-637},
  author = {Stanford, J.L. and Gunthorpe, W.J.},
  title = {A study of some fast-growing scotochromogenic mycobacteria including species descriptions of \textit{Mycobacterium gilvum} (new species) and \textit{Mycobacterium} duv alii (new species).},
  issue = {6},
  pmid = {5002706}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{TsukamuraEtAl1981a,
  year = {1981},
  journal = {Int. J. Syst. Bacteriol.},
  volume = {31},
  pages = {263-275},
  author = {Tsukamura, M. and Mizuno, S. and Tsukamura, S.},
  title = {Numerical analysis of rapidly growing, scotochromogenic mycobacteria, including \textit{Mycobacterium obuense} sp. nov., nom. rev., \textit{Mycobacterium rhodesiae} sp. nov., nom. rev., \textit{Mycobacterium aichiense} sp. nov., nom. rev., \textit{Mycobacterium chubuense} sp. nov., nom. rev., and \textit{Mycobacterium tokaiense} sp. nov., nom. rev.},
  doi = {10.1099/00207713-31-3-263},
  issue = {3}
}


@article{ThorelEtAl1990a,
  year = {1990},
  journal = {Int J Syst Bacteriol},
  volume = {40},
  pages = {254-260},
  author = {Thorel, M.F. and Krichevsky, M. and Levy-Frebault, V.V.},
  title = {Numerical taxonomy of mycobactin-dependent mycobacteria, emended description of \textit{Mycobacterium avium}, and description of \textit{Mycobacterium avium} subsp. \textit{avium} subsp. nov., \textit{Mycobacterium avium} subsp. \textit{paratuberculosis} subsp. nov., and \textit{Mycobacterium avium} subsp. \textit{silvaticum} subsp. nov.},
  abstract = {We performed a numerical taxonomy analysis of 38 \textit{Mycobacterium paratuberculosis} and related mycobacterial strains, including wood pigeon mycobacteria; this analysis was based on 22 tests, which were selected for their potential discriminative value from a total of 51 tests studied and produced four well-defined clusters. Cluster 1 contained the \textit{M. paratuberculosis} strains, including two strains isolated from Crohn's disease patients; cluster 2 contained \textit{Mycobacterium avium} and \textit{Mycobacterium intracellulare} reference strains; cluster 3 consisted of the wood pigeon mycobacteria; and the only strain in cluster 4 was \textit{M. paratuberculosis} 316F, which is used for antigen and vaccine production. Strains in cluster 1 were mycobactin dependent even when they were subcultured, whereas strains in cluster 3 were unable to grow on egg medium and their growth was stimulated by pH 5.5. Growth stimulation by pyruvate, resistance to D-cycloserine (50 micrograms/ml), and alkaline phosphatase activity also were characteristics that were useful for discriminating between clusters 1 and 3. The results of previous DNA-DNA hybridization studies have demonstrated that \textit{M. avium} Chester 1901, \textit{M. paratuberculosis} Bergey et al. 1923, and the wood pigeon mycobacteria belong to a single genomic species, and we propose that the name of this species should be \textit{M. avium}. On the basis of the results of previous genomic analyses based on restriction fragment length, the results of polymorphism studies, and DNA patterns determined by field inversion gel electrophoresis as well as the results of our phenotypic study, we propose that the species should be divided into subspecies which correspond to pathogenicity and host range characteristics.(ABSTRACT TRUNCATED AT 250 WORDS)},
  doi = {10.1099/00207713-40-3-254},
  issue = {3},
  pmid = {2397193}
}


@article{NouiouiEtAl2018j,
  year = {2018},
  journal = {Antonie Van Leeuwenhoek},
  volume = {111},
  pages = {1209-1223},
  author = {Nouioui, I. and Carro, L. and Sangal, V. and Jando, M. and Igual, J.M. and Goodfellow, M. and Klenk, H.P.},
  title = {Formal description of \textit{Mycobacterium neglectum} sp. nov. and \textit{Mycobacterium palauense} sp. nov., rapidly growing actinobacteria.},
  abstract = {The taxonomic positions of two fast growing mycobacteria (CECT 8778\textsuperscript{T} and CECT 8779\textsuperscript{T}) were established using a polyphasic approach. The strains were shown to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus \textit{Mycobacterium}. Multi-locus sequence analyses (MLSA) show that strain CECT 8778\textsuperscript{T} forms a well-supported clade together with the type strains of \textit{Mycobacterium aurum}, \textit{Mycobacterium austroafricanum} and \textit{Mycobacterium vanbaalenii} while strain CECT 8779\textsuperscript{T} presents as a distinct branch that is well separated from its near phylogenetic neighbours; it is also apparent from the MLSA genetic distances that these strains are most closely related to the type strains of \textit{Mycobacterium mageritense} and \textit{M. vanbaalenii}, respectively. Digital DNA:DNA hybridization and average nucleotide identity values between each of the strains and its close phylogenetic neighbour are below the 70 and 96% threshold values for definition of prokaryotic species; these results are underpinned by corresponding phenotypic data. Based upon the consensus of the phenotypic and phylogenetic analyses, it can be concluded that the two strains represent novel species within the genus \textit{Mycobacterium} for which the following names are proposed: \textit{Mycobacterium neglectum} sp. nov., with the type strain CECT 8778\textsuperscript{T} (BN 3150\textsuperscript{T} = DSM 44756\textsuperscript{T}) and \textit{Mycobacterium palauense} sp. nov., with the type strain CECT 8779\textsuperscript{T} (= DSM 44914\textsuperscript{T}).},
  doi = {10.1007/s10482-018-1029-5},
  issue = {7},
  pmid = {29404824}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{SchinskyEtAl2004a,
  year = {2004},
  journal = {Int J Syst Evol Microbiol},
  volume = {54},
  pages = {1653-1667},
  author = {Schinsky, M.F. and Morey, R.E. and Steigerwalt, A.G. and Douglas, M.P. and Wilson, R.W. and Floyd, M.M. and Butler, W.R. and Daneshvar, M.I. and Brown-Elliott, B.A. and Wallace, R.J.J. and McNeil, M.M. and Brenner, D.J. and Brown, J.M.},
  title = {Taxonomic variation in the \textit{Mycobacterium fortuitum} third biovariant complex: description of \textit{Mycobacterium boenickei} sp. nov., \textit{Mycobacterium houstonense} sp. nov., \textit{Mycobacterium neworleansense} sp. nov. and \textit{Mycobacterium brisbanense} sp. nov. and recognition of \textit{Mycobacterium porcinum} from human clinical isolates.},
  abstract = {The \textit{Mycobacterium fortuitum} third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of \textit{M. fortuitum} third biovariant complex sorbitol-negative (n = 21), \textit{M. fortuitum} third biovariant complex sorbitol-positive (n = 3), \textit{M. fortuitum} (n = 3), \textit{Mycobacterium peregrinum} (pipemidic acid-susceptible) (n = 1), \textit{Mycobacterium porcinum} (n = 1), \textit{Mycobacterium senegalense} (n = 2) and \textit{Mycobacterium septicum} (n = 1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G + C content and DNA-DNA relatedness analyses. The results of these studies indicated that the strains comprised \textit{M. porcinum} (n = 13), \textit{M. septicum} (n = 1) and four novel closely related genetic groups within the \textit{M. fortuitum} third biovariant complex: \textit{Mycobacterium boenickei} sp. nov. (n = 6), \textit{Mycobacterium houstonense} sp. nov. (n = 2), \textit{Mycobacterium neworleansense} sp. nov. (n = 1) and \textit{Mycobacterium brisbanense} sp. nov. (n = 1), with type strains ATCC 49935T (= W5998T = DSM 44677T), ATCC 49403T (= W5198T = DSM 44676T) ATCC 49404T (= W6705T = DSM 44679T) and ATCC 49938T (= W6743T = DSM 44680T), respectively.},
  doi = {10.1099/ijs.0.02743-0},
  issue = {5},
  pmid = {15388725}
}


@article{LeeEtAl2016m,
  year = {2016},
  journal = {Int J Syst Evol Microbiol},
  volume = {66},
  pages = {3132-3141},
  author = {Lee, S.Y. and Kim, B.J. and Kim, H. and Won, Y.S. and Jeon, C.O. and Jeong, J. and Lee, S.H. and Lim, J.H. and Lee, S.H. and Kim, C.K. and Kook, Y.H. and Kim, B.J.},
  title = {\textit{Mycobacterium paraintracellulare} sp. nov., for the genotype INT-1 of \textit{Mycobacterium intracellulare}.},
  abstract = {Three mycobacterial strains, isolated from independent Korean patients with pulmonary infections, belonging to the \textit{Mycobacterium intracellulare} genotype 1 (INT-1) were characterized using a polyphasic approach. The sequences of the 16S rRNA gene and internal transcribed spacer 1 (ITS1) of the INT-1 strains were identical to those of \textit{Mycobacterium intracellulare} ATCC 13950T. However, multilocus sequence typing (MLST) analysis targeting five housekeeping genes (hsp65, rpoB, argG, gnd and pgm) revealed the phylogenetic separation of these strains from \textit{M. intracellulare} ATCC 13950T. DNA-DNA hybridization values of >70 % confirmed that the three isolates belong to the same species, while the values of <70 % between one of them and the type strains of \textit{M. intracellulare} and \textit{Mycobacterium chimaera} confirmed their belonging to a distinct species. In addition, phenotypic characteristics such as positive growth on MacConkey agar and in acidic broth culture, unique matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS profiles of lipids, and unique mycolic acids profiles further supported the taxonomic status of these strains as representatives of a novel species of the \textit{Mycobacterium avium} complex named \textit{Mycobacterium paraintracellulare}. The type strain is MOTT64T (=KCTC 29084T=JCM 30622T).},
  doi = {10.1099/ijsem.0.001158},
  issue = {8},
  pmid = {27189351}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{BensalahEtAl2009a,
  year = {2009},
  journal = {Int J Syst Evol Microbiol},
  volume = {59},
  pages = {2803-2808},
  author = {Ben Salah, I. and Cayrou, C. and Raoult, D. and Drancourt, M.},
  title = {\textit{Mycobacterium marseillense} sp. nov., \textit{Mycobacterium timonense} sp. nov. and \textit{Mycobacterium bouchedurhonense} sp. nov., members of the \textit{Mycobacterium avium} complex.},
  abstract = {An rpoB sequence-based evaluation of 100 \textit{Mycobacterium avium} complex (MAC) clinical isolates led to the identification of five respiratory tract isolates that were potential representatives of three novel MAC species. Distinctive phenotypic features of isolates 62863 and 5356591\textsuperscript{T} included a pseudomycelium morphology and both esterase and acid phosphatase activities. These two isolates exhibited sequence similarities of 99.8 % for the 16S rRNA gene, 86.3 and 86.1 % for 16S-23S rRNA gene internal transcribed spacer (ITS-1) sequence, 96.7 and 97.8 % for rpoB and 97.6 and 97.4 % for hsp65, respectively, with the type strain of \textit{Mycobacterium chimaera}, the most closely related species. Isolates 3256799 and 5351974\textsuperscript{T} lacked alpha-mannosidase and beta-glucosidase activities. They exhibited sequence similarities of 99.6 % for the 16S rRNA gene, 90.1 and 90.4 % for ITS-1, 97.8 % for rpoB and 98.0 and 98.1 % for hsp65, respectively, with the type strain of \textit{M. chimaera}, the most closely related species. Isolate 4355387\textsuperscript{T} lacked urease and alpha-glucosidase activities, but it exhibited valine arylamidase, cystine arylamidase and acid phosphatase activities. It had sequence similarities of 99.3 % for the 16S rRNA gene, 51.8 % for ITS-1, 97.1 % for rpoB and 97.8 % for hsp65 with the type strain of \textit{Mycobacterium colombiense}, the most closely related species. A phylogenetic tree based on concatenated 16S rRNA gene, ITS-1, rpoB and hsp65 sequences showed the uniqueness of these five isolates as representatives of three novel species, with bootstrap values >/=95 % in all nodes. On the basis of these phenotypic and genetic characteristics, these five isolates are proposed as representatives of three novel MAC species: \textit{Mycobacterium marseillense} sp. nov., with strain 5356591\textsuperscript{T} (=CCUG 56325\textsuperscript{T} =CIP 109828\textsuperscript{T} =CSUR P30\textsuperscript{T}) as the type strain; \textit{Mycobacterium timonense} sp. nov., with strain 5351974\textsuperscript{T} (=CCUG 56329\textsuperscript{T} =CIP 109830\textsuperscript{T} =CSUR P32\textsuperscript{T}) as the type strain; and \textit{Mycobacterium bouchedurhonense} sp. nov., with strain 4355387\textsuperscript{T} (=CCUG 56331\textsuperscript{T} =CIP 109827\textsuperscript{T} =CSUR P34\textsuperscript{T}) as the type strain.},
  doi = {10.1099/ijs.0.010637-0},
  issue = {11},
  pmid = {19628609}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{BensalahEtAl2009a,
  year = {2009},
  journal = {Int J Syst Evol Microbiol},
  volume = {59},
  pages = {2803-2808},
  author = {Ben Salah, I. and Cayrou, C. and Raoult, D. and Drancourt, M.},
  title = {\textit{Mycobacterium marseillense} sp. nov., \textit{Mycobacterium timonense} sp. nov. and \textit{Mycobacterium bouchedurhonense} sp. nov., members of the \textit{Mycobacterium avium} complex.},
  abstract = {An rpoB sequence-based evaluation of 100 \textit{Mycobacterium avium} complex (MAC) clinical isolates led to the identification of five respiratory tract isolates that were potential representatives of three novel MAC species. Distinctive phenotypic features of isolates 62863 and 5356591\textsuperscript{T} included a pseudomycelium morphology and both esterase and acid phosphatase activities. These two isolates exhibited sequence similarities of 99.8 % for the 16S rRNA gene, 86.3 and 86.1 % for 16S-23S rRNA gene internal transcribed spacer (ITS-1) sequence, 96.7 and 97.8 % for rpoB and 97.6 and 97.4 % for hsp65, respectively, with the type strain of \textit{Mycobacterium chimaera}, the most closely related species. Isolates 3256799 and 5351974\textsuperscript{T} lacked alpha-mannosidase and beta-glucosidase activities. They exhibited sequence similarities of 99.6 % for the 16S rRNA gene, 90.1 and 90.4 % for ITS-1, 97.8 % for rpoB and 98.0 and 98.1 % for hsp65, respectively, with the type strain of \textit{M. chimaera}, the most closely related species. Isolate 4355387\textsuperscript{T} lacked urease and alpha-glucosidase activities, but it exhibited valine arylamidase, cystine arylamidase and acid phosphatase activities. It had sequence similarities of 99.3 % for the 16S rRNA gene, 51.8 % for ITS-1, 97.1 % for rpoB and 97.8 % for hsp65 with the type strain of \textit{Mycobacterium colombiense}, the most closely related species. A phylogenetic tree based on concatenated 16S rRNA gene, ITS-1, rpoB and hsp65 sequences showed the uniqueness of these five isolates as representatives of three novel species, with bootstrap values >/=95 % in all nodes. On the basis of these phenotypic and genetic characteristics, these five isolates are proposed as representatives of three novel MAC species: \textit{Mycobacterium marseillense} sp. nov., with strain 5356591\textsuperscript{T} (=CCUG 56325\textsuperscript{T} =CIP 109828\textsuperscript{T} =CSUR P30\textsuperscript{T}) as the type strain; \textit{Mycobacterium timonense} sp. nov., with strain 5351974\textsuperscript{T} (=CCUG 56329\textsuperscript{T} =CIP 109830\textsuperscript{T} =CSUR P32\textsuperscript{T}) as the type strain; and \textit{Mycobacterium bouchedurhonense} sp. nov., with strain 4355387\textsuperscript{T} (=CCUG 56331\textsuperscript{T} =CIP 109827\textsuperscript{T} =CSUR P34\textsuperscript{T}) as the type strain.},
  doi = {10.1099/ijs.0.010637-0},
  issue = {11},
  pmid = {19628609}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{LeeEtAl2010a,
  year = {2010},
  journal = {Int J Syst Evol Microbiol},
  volume = {60},
  pages = {439-443},
  author = {Lee, H.K. and Lee, S.A. and Lee, I.K. and Yu, H.K. and Park, Y.G. and Hyun, J.W. and Kim, K. and Kook, Y.H. and Kim, B.J.},
  title = {\textit{Mycobacterium paraseoulense} sp. nov., a slowly growing, scotochromogenic species related genetically to \textit{Mycobacterium seoulense}.},
  abstract = {A previously unidentified, slowly growing, scotochromogenic \textit{Mycobacterium} species, represented by strain 31118\textsuperscript{T}, was discovered during hsp65 sequence-based reidentification of Korean clinical isolates that had been previously identified as \textit{Mycobacterium scrofulaceum} by conventional biochemical tests. Although the 16S rRNA gene sequence of strain 31118\textsuperscript{T} was identical to that of the recently described \textit{Mycobacterium seoulense}, phylogenetic analyses based on three independent alternative targets (rpoB, hsp65 and the 16S-23S internal transcribed spacer) showed that it was closely related to \textit{M. seoulense} but was a distinct phylogenetic entity. Furthermore, the phenetic characteristics of this strain were more similar to those of \textit{M. scrofulaceum} than to those of \textit{M. seoulense}. Taken together, these results support the conclusion that this strain represents a novel mycobacterium species, for which the name \textit{Mycobacterium paraseoulense} sp. nov. is proposed. The type strain is 31118\textsuperscript{T} (=DSM 45000\textsuperscript{T} =KCTC 19145\textsuperscript{T}).},
  doi = {10.1099/ijs.0.012054-0},
  issue = {2},
  pmid = {19654367}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{BangEtAl2008a,
  year = {2008},
  journal = {Int J Syst Evol Microbiol},
  volume = {58},
  pages = {2398-2402},
  author = {Bang, D. and Herlin, T. and Stegger, M. and Andersen, A.B. and Torkko, P. and Tortoli, E. and Thomsen, V.O.},
  title = {\textit{Mycobacterium arosiense} sp. nov., a slowly growing, scotochromogenic species causing osteomyelitis in an immunocompromised child.},
  abstract = {A yellow-pigmented, scotochromogenic, slowly growing mycobacterial strain, designated T1921\textsuperscript{T}, was isolated from the disseminated osteomyelitic lesions of a 7-year-old child with an underlying partial gamma interferon receptor alpha-1 deficiency. Hybridization by the line probe assay indicated the presence of a \textit{Mycobacterium} species. Sequencing of the 16S rRNA gene, the internally transcribed spacer (ITS) region and the hsp65 and rpoB genes revealed that strain T1921\textsuperscript{T} could be differentiated from all recognized species of the genus \textit{Mycobacterium}. Phylogenetic analysis based on the 16S rRNA gene indicated that strain T1921\textsuperscript{T} was related most closely to \textit{Mycobacterium intracellulare}, whereas analysis based on the ITS and hsp65 and rpoB genes indicated that it was most closely related to \textit{Mycobacterium avium}. Phenotypic tests were not able to differentiate strain T1921\textsuperscript{T} from similar slowly growing mycobacteria. Strain T1921\textsuperscript{T} is considered to represent a novel species of the genus \textit{Mycobacterium}, for which the name \textit{Mycobacterium arosiense} sp. nov. is proposed. The type strain is T1921\textsuperscript{T} (=DSM 45069\textsuperscript{T} =ATCC BAA-1401\textsuperscript{T}).},
  doi = {10.1099/ijs.0.65503-0},
  issue = {10},
  pmid = {18842863}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{BrownEtAl1999b,
  year = {1999},
  journal = {Int J Syst Bacteriol},
  volume = {49},
  pages = {1493-1511},
  author = {Brown, B.A. and Springer, B. and Steingrube, V.A. and Wilson, R.W. and Pfyffer, G.E. and Garcia, M.J. and Menendez, M.C. and Rodriguez-Salgado, B. and Jost, K.C.J. and Chiu, S.H. and Onyi, G.O. and Bottger, E.C. and Wallace, R.J.J.},
  title = {\textit{Mycobacterium wolinskyi} sp. nov. and \textit{Mycobacterium goodii} sp. nov., two new rapidly growing species related to \textit{Mycobacterium smegmatis} and associated with human wound infections: a cooperative study from the International Working Group on Mycobacterial Taxonomy.},
  abstract = {Previous investigations demonstrated three taxonomic groups among 22 clinical isolates of \textit{Mycobacterium smegmatis}. These studies were expanded to 71 clinical isolates, of which 35 (49%) (group 1) were identical to five ATCC reference strains including the type strain ATCC 19420T. Twenty-eight isolates (39%) were group 2, and eight isolates (11%) were group 3. Isolates of groups 2 and 3 were most often associated with post-traumatic or post-surgical wound infections including osteomyelitis, were susceptible to sulfamethoxazole, amikacin, imipenem and the tetracyclines, variably resistant to clarithromycin, and susceptible (group 1), intermediately resistant (group 2) or resistant (group 3) to tobramycin. The three groups were similar by routine biochemical and growth characteristics, but had different mycolic acid dimethoxy-4-coumarinylmethyl ester elution patterns by HPLC and different PCR-restriction enzyme patterns of a 439 bp fragment of the hsp-65 gene. Group 3 isolates differed from group 1 by 18 bp by 16S rRNA sequencing and exhibited < 25% homology by DNA-DNA hybridization, being most closely related to \textit{Mycobacterium mageritense}. The 16S rRNA of group 1 and group 2 isolates differed by only 3 bp, but by DNA-DNA hybridization they exhibited only 40% homology. The following names are proposed: \textit{Mycobacterium goodii} sp. nov. for group 2 isolates (type strain ATCC 700504T = MO69T), \textit{Mycobacterium wolinskyi} sp. nov. for group 3 isolates (type strain ATCC 700010T = MO739T) and \textit{Mycobacterium smegmatis} sensu stricto for group 1 isolates.},
  doi = {10.1099/00207713-49-4-1493},
  issue = {4},
  pmid = {10555330}
}

@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{VaningenEtAl2009d,
  year = {2009},
  journal = {Int J Syst Evol Microbiol},
  volume = {59},
  pages = {2277-2282},
  author = {van Ingen, J. and Boeree, M.J. and Kosters, K. and Wieland, A. and Tortoli, E. and Dekhuijzen, P.N. and van Soolingen, D.},
  title = {Proposal to elevate \textit{Mycobacterium avium} complex ITS sequevar MAC-Q to \textit{Mycobacterium vulneris} sp. nov.},
  abstract = {The \textit{Mycobacterium avium} complex (MAC) consists of four recognized species, \textit{Mycobacterium avium}, \textit{Mycobacterium colombiense}, \textit{Mycobacterium intracellulare} and \textit{Mycobacterium chimaera}, and a variety of other strains that may be members of undescribed taxa. We report on two isolates of a scotochromogenic, slowly growing, non-tuberculous \textit{Mycobacterium} species within the \textit{M. avium} complex from a lymph node and an infected wound after a dogbite of separate patients in The Netherlands. The extrapulmonary infections in immunocompetent patients suggested a high level of virulence. These isolates were characterized by a unique nucleotide sequence in the 16S rRNA gene, 99% similar to \textit{Mycobacterium colombiense}, and the MAC-Q 16S-23S internal transcribed spacer (ITS) sequence. Sequence analyses of the hsp65 gene revealed 97% similarity to \textit{M. avium}. The rpoB gene sequence was 98% similar to \textit{M. colombiense}. Phenotypically, the scotochromogenicity, positive semi-quantitative catalase and heat-stable catalase tests, negative tellurite reductase and urease tests and susceptibility to hydroxylamine and oleic acid set these isolates apart from related species. High-performance liquid chromatography analysis of cell-wall mycolic acid content revealed a unique pattern, related to that of \textit{M. avium} and \textit{M. colombiense}. Together, these findings supported a separate species status within the \textit{Mycobacterium avium} complex. We propose elevation of scotochromogenic \textit{M. avium} complex strains sharing this 16S gene and MAC-Q ITS sequence to separate species status, for which the name \textit{Mycobacterium vulneris} sp. nov. is proposed. The type strain is NLA000700772T (=DSM 45247T=CIP 109859T).},
  doi = {10.1099/ijs.0.008854-0},
  issue = {9},
  pmid = {19620376}
}


@article{MohamedEtAl2004a,
  year = {2004},
  journal = {Int J Syst Evol Microbiol},
  volume = {54},
  pages = {2057-2060},
  author = {Mohamed, A.M. and Iwen, P.C. and Tarantolo, S. and Hinrichs, S.H.},
  title = {\textit{Mycobacterium nebraskense} sp. nov., a novel slowly growing scotochromogenic species.},
  abstract = {The characterization of a novel slowly growing, scotochromogenic \textit{Mycobacterium} species is reported. This previously undescribed mycobacterial species was isolated from five different patients with symptomatic pulmonary infections. All isolates were acid-fast-positive and the mycolic acid profiles were unique and supported placement into the genus \textit{Mycobacterium}. Phenotypic characteristics of each strain included optimal growth after 3 weeks at a temperature range of 30-35 degrees C, yellow pigmentation after incubation in the dark and production of a heat-stable catalase. The 16S rRNA gene and internal transcribed spacer 1 sequences were identical for all five strains, but distinct from all known mycobacterial species. Phylogenetic analysis based on the 16S rRNA gene sequence placed the novel species within the slowly growing mycobacteria group in close proximity to \textit{Mycobacterium malmoense}, \textit{Mycobacterium avium}, \textit{Mycobacterium kansasii} and \textit{Mycobacterium scrofulaceum}. These data support the conclusion that the related five described organisms represent a novel \textit{Mycobacterium} species, for which the name \textit{Mycobacterium nebraskense} sp. nov. is proposed, with the type strain UNMC-MY1349\textsuperscript{T} (=ATCC BAA-837\textsuperscript{T}=DSM 44803\textsuperscript{T}).},
  doi = {10.1099/ijs.0.63126-0},
  issue = {6},
  pmid = {15545434}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{JimenezEtAl2004a,
  year = {2004},
  journal = {Int J Syst Evol Microbiol},
  volume = {54},
  pages = {1729-1734},
  author = {Jimenez, M.S. and Campos-Herrero, M.I. and Garcia, D. and Luquin, M. and Herrera, L. and Garcia, M.J.},
  title = {\textit{Mycobacterium canariasense} sp. nov.},
  abstract = {A novel rapidly growing, non-pigmented mycobacterium was isolated from blood samples obtained from 17 patients with febrile syndrome. Bacterial growth occurred at 30 and 37 degrees C on Lowenstein-Jensen medium and also on MacConkey agar without crystal violet. Strains contained alpha- and alpha'-mycolates in their cell wall. Sequence analysis of the hsp65 and 16S rRNA genes identified the isolates as rapidly growing mycobacteria. Sequences of both genes were unique within the mycobacteria. DNA-DNA hybridization showed that the isolates had less than 15 % reassociation with 13 other recognized rapidly growing mycobacteria. The name \textit{Mycobacterium canariasense} sp. nov. is proposed for this novel opportunistic pathogen, which is most closely related to \textit{Mycobacterium diernhoferi}. The type strain is 502329T (= CIP 107998T = CCUG 47953T).},
  doi = {10.1099/ijs.0.02999-0},
  issue = {5},
  pmid = {15388736}
}


@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{TurenneEtAl2002a,
  year = {2002},
  journal = {Int J Syst Evol Microbiol},
  volume = {52},
  pages = {2135-2140},
  author = {Turenne, C. and Chedore, P. and Wolfe, J. and Jamieson, F. and Broukhanski, G. and May, K. and Kabani, A.},
  title = {\textit{Mycobacterium lacus} sp. nov., a novel slowly growing, non-chromogenic clinical isolate.},
  abstract = {A strain of a novel non-chromogenic mycobacterium was isolated from synovial tissue from a 68-year-old female with bursitis of her right elbow. The slowly growing strain had a unique PCR-restriction enzyme analysis (PRA) profile of the hsp65 gene and 16S rRNA gene sequence in comparison with other mycobacterium species. The most closely related species, as determined by 16S rRNA gene sequence analysis, are \textit{Mycobacterium malmoense}, \textit{Mycobacterium marinum}, \textit{Mycobacterium ulcerans} and members of the \textit{Mycobacterium tuberculosis} complex. The HPLC and biochemical profiles resembled those of \textit{Mycobacterium gastri}, although differences were noted in the peak-height ratio of the HPLC pattern and the nitrate and pyrazinamidase tests. On the basis of PRA, HPLC, biochemical and 16S rRNA gene sequence analyses, the name \textit{Mycobacterium lacus} sp. nov. is proposed for this potential pathogen. The type strain is strain NRCM 00-255\textsuperscript{T} (= ATCC BAA-323\textsuperscript{T} = DSM 44577\textsuperscript{T}).},
  doi = {10.1099/00207713-52-6-2135},
  issue = {6},
  pmid = {12508880}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{KusunokiEzaki1992a,
  year = {1992},
  journal = {Int J Syst Bacteriol},
  volume = {42},
  pages = {240-245},
  author = {Kusunoki, S. and Ezaki, T.},
  title = {Proposal of \textit{Mycobacterium peregrinum} sp. nov., nom. rev., and elevation of \textit{Mycobacterium chelonae} subsp. \textit{abscessus} (Kubica et al.) to species status: \textit{Mycobacterium abscessus} comb. nov.},
  abstract = {We studied the taxonomic positions of the rapidly growing organism \textit{Mycobacterium fortuitum} and phenotypically related organisms. We confirmed that "\textit{Mycobacterium peregrinum}" ATCC 14467T (T = type strain) is genetically independent of \textit{M. fortuitum} ATCC 6841T by using various DNA hybridization conditions. Strains that were genetically identified as "\textit{M. peregrinum}" were phenotypically differentiated from \textit{M. fortuitum} ATCC 6841T. Thus, we propose that "\textit{M. peregrinum}" should be revived as an independent species, \textit{Mycobacterium peregrinum} sp. nov., nom. rev. The type strain is strain ATCC 14467. \textit{M. fortuitum} subsp. \textit{acetamidolyticum} ATCC 35931T exhibited a high level of DNA relatedness to \textit{M. fortuitum} ATCC 6841T. The hybridized DNAs maintained stable heteroduplexity at high stringency; thus, we confirmed that \textit{M. fortuitum} subsp. \textit{acetamidolyticum} is identical to \textit{M. fortuitum} ATCC 6841T. We found that \textit{M. chelonae} subsp. \textit{abscessus} ATCC 19977T is genetically different from \textit{M. chelonae} subsp. \textit{chelonae} NCTC 946T on the basis of the results of quantitative hybridization even under optimal conditions. There was no reason to maintain this organism as a subspecies of \textit{M. chelonae}. Thus, we propose that \textit{M. chelonae} subsp. \textit{abscessus} should be elevated to species status as \textit{Mycobacterium abscessus} (Kubica et al.) comb. nov. The type strain is strain ATCC 19977.},
  doi = {10.1099/00207713-42-2-240},
  issue = {2},
  pmid = {1581184}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{MarksEtAl1972a,
  year = {1972},
  journal = {Tubercle},
  volume = {53},
  pages = {210-214},
  author = {Marks, J. and Jenkins, P.A. and Tsukamura, M.},
  title = {\textit{Mycobacterium szulgai}--a new pathogen.},
  doi = {10.1016/0041-3879(72)90018-9},
  issue = {3},
  pmid = {4673103}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{Wayne1966a,
  year = {1966},
  journal = {Am Rev Respir Dis},
  volume = {93},
  pages = {919-928},
  author = {Wayne, L.G.},
  title = {Classification and identification of mycobacteria. 3. Species within group 3.},
  doi = {10.1164/arrd.1966.93.6.919},
  issue = {6},
  pmid = {5942239}
}


@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{TortoliEtAl2004a,
  year = {2004},
  journal = {Int J Syst Evol Microbiol},
  volume = {54},
  pages = {1277-1285},
  author = {Tortoli, E. and Rindi, L. and Garcia, M.J. and Chiaradonna, P. and Dei, R. and Garzelli, C. and Kroppenstedt, R.M. and Lari, N. and Mattei, R. and Mariottini, A. and Mazzarelli, G. and Murcia, M.I. and Nanetti, A. and Piccoli, P. and Scarparo, C.},
  title = {Proposal to elevate the genetic variant MAC-A, included in the \textit{Mycobacterium avium} complex, to species rank as \textit{Mycobacterium chimaera} sp. nov.},
  abstract = {The possibility that the strains included within the \textit{Mycobacterium avium} complex (MAC), but not belonging either to \textit{M. avium} or to \textit{Mycobacterium intracellulare}, may be members of undescribed taxa, has already been questioned by several taxonomists. A very homogeneous cluster of 12 strains characterized by identical nucleotide sequences both in the 16S rDNA and in the 16S-23S internal transcribed spacer was investigated. Similar strains, previously reported in the literature, had been assigned either to the species \textit{M. intracellulare} on the basis of the 16S rDNA similarity or to the group of MAC intermediates. However, several phenotypical and epidemiological characteristics seem to distinguish these strains from all other MAC organisms. The unique mycolic acid pattern obtained by HPLC is striking as it is characterized by two clusters of peaks, instead of the three presented by all other MAC organisms. All of the strains have been isolated from humans and all but one came from the respiratory tract of elderly people. The clinical significance of these strains, ascertained for seven patients, seems to suggest an unusually high virulence. The characteristics of all the strains reported in the literature, genotypically identical to the ones described here, seem to confirm our data, without reports of isolations from animals or the environment or, among humans, from AIDS patients. Therefore, an elevation of the MAC variant was proposed and characterized here, with the name \textit{Mycobacterium chimaera} sp. nov.; this increases the number of species included in the \textit{M. avium} complex. The type strain is FI-01069T (=CIP 107892T=DSM 44623T).},
  doi = {10.1099/ijs.0.02777-0},
  issue = {4},
  pmid = {15280303}
}


@article{ShahrakiEtAl2017a,
  year = {2017},
  journal = {Int J Syst Evol Microbiol},
  volume = {67},
  pages = {1766-1770},
  author = {Shahraki, A.H. and Trovato, A. and Mirsaeidi, M. and Borroni, E. and Heidarieh, P. and Hashemzadeh, M. and Shahbazi, N. and Cirillo, D.M. and Tortoli, E.},
  title = {\textit{Mycobacterium persicum} sp. nov., a novel species closely related to \textit{Mycobacterium kansasii} and \textit{Mycobacterium gastri}.},
  abstract = {Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel \textit{Mycobacterium} species. Similarity, at the phenotypic level, with \textit{Mycobacterium kansasii} is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is \textit{Mycobacterium persicum} sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain.},
  doi = {10.1099/ijsem.0.001862},
  issue = {6},
  pmid = {28629501}
}


@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{ReischlEtAl1998b,
  year = {1998},
  journal = {Int J Syst Bacteriol},
  volume = {48},
  pages = {1349-1355},
  author = {Reischl, U. and Emler, S. and Horak, Z. and Kaustova, J. and Kroppenstedt, R.M. and Lehn, N. and Naumann, L.},
  title = {\textit{Mycobacterium bohemicum} sp. nov., a new slow-growing scotochromogenic mycobacterium.},
  abstract = {A new, slow-growing, scotochromogenic mycobacterium was isolated from sputum of a 53-year-old patient with Down's syndrome suffering from tuberculosis. Growth occurred at temperatures between 25 and 40 degrees C with an optimum at 37 degrees C. This strain had surprisingly few enzymic activities (only positive for 68 degrees C heat-stable catalase and weakly positive for urease) and was sensitive to prothionamide, cycloserine, clarithromycin, gentamicin and amikacin but showed resistance to isoniazid, streptomycin, ethambutol, rifampin and ciprofloxacin. These characteristics assign this organism to a novel mycobacterial species characterized by a unique 16S rDNA nucleotide sequence. The name \textit{Mycobacterium bohemicum} sp. nov. is proposed for this new, slow-growing, scotochromogenic mycobacterium. The type strain is DSM 44277T.},
  doi = {10.1099/00207713-48-4-1349},
  issue = {4},
  pmid = {9828436}
}


@article{DomenechEtAl1997a,
  year = {1997},
  journal = {Int J Syst Bacteriol},
  volume = {47},
  pages = {535-540},
  author = {Domenech, P. and Jimenez, M.S. and Menendez, M.C. and Bull, T.J. and Samper, S. and Manrique, A. and Garcia, M.J.},
  title = {\textit{Mycobacterium mageritense} sp. nov.},
  abstract = {Strains of a new species of rapidly growing, nonphotochromogenic mycobacteria, \textit{Mycobacterium mageritense}, were isolated from human sputum. The growth characteristics, acid fastness, and mycolic acids of the isolates were consistent with those of \textit{Mycobacterium} species. The isolates were identified as members of a new species by performing a biochemical analysis and DNA-DNA hybridization experiments, and by comparing the sequences of several conserved genes, such as the 16S rRNA, hsp65, and sodA genes. A phylogenetic analysis in which 16S rRNA and sodA sequences were used identified \textit{M. mageritense} as a novel distinct species and placed \textit{M. mageritense} between members of the \textit{Mycobacterium fortuitum} complex and the thermotolerant rapidly growing group. Our results demonstrate that the taxonomic value of sodA sequence analysis in the genus \textit{Mycobacterium} is similar to the well-established value of 16S rRNA sequence analysis.},
  doi = {10.1099/00207713-47-2-535},
  issue = {2},
  pmid = {9103645}
}

@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{SompolinskyEtAl1978a,
  year = {1978},
  journal = {International Journal of Systematic Bacteriology},
  volume = {28},
  pages = {67-75},
  author = {Sompolinsky, D. and Lagziel, A. and Naveh, D. and Yankilevitz, L.},
  title = {\textit{M. haemophilum} sp. nov., a new pathogen of humans.},
  doi = {10.1099/00207713-28-1-67},
  issue = {1}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{SchinskyEtAl2004a,
  year = {2004},
  journal = {Int J Syst Evol Microbiol},
  volume = {54},
  pages = {1653-1667},
  author = {Schinsky, M.F. and Morey, R.E. and Steigerwalt, A.G. and Douglas, M.P. and Wilson, R.W. and Floyd, M.M. and Butler, W.R. and Daneshvar, M.I. and Brown-Elliott, B.A. and Wallace, R.J.J. and McNeil, M.M. and Brenner, D.J. and Brown, J.M.},
  title = {Taxonomic variation in the \textit{Mycobacterium fortuitum} third biovariant complex: description of \textit{Mycobacterium boenickei} sp. nov., \textit{Mycobacterium houstonense} sp. nov., \textit{Mycobacterium neworleansense} sp. nov. and \textit{Mycobacterium brisbanense} sp. nov. and recognition of \textit{Mycobacterium porcinum} from human clinical isolates.},
  abstract = {The \textit{Mycobacterium fortuitum} third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of \textit{M. fortuitum} third biovariant complex sorbitol-negative (n = 21), \textit{M. fortuitum} third biovariant complex sorbitol-positive (n = 3), \textit{M. fortuitum} (n = 3), \textit{Mycobacterium peregrinum} (pipemidic acid-susceptible) (n = 1), \textit{Mycobacterium porcinum} (n = 1), \textit{Mycobacterium senegalense} (n = 2) and \textit{Mycobacterium septicum} (n = 1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G + C content and DNA-DNA relatedness analyses. The results of these studies indicated that the strains comprised \textit{M. porcinum} (n = 13), \textit{M. septicum} (n = 1) and four novel closely related genetic groups within the \textit{M. fortuitum} third biovariant complex: \textit{Mycobacterium boenickei} sp. nov. (n = 6), \textit{Mycobacterium houstonense} sp. nov. (n = 2), \textit{Mycobacterium neworleansense} sp. nov. (n = 1) and \textit{Mycobacterium brisbanense} sp. nov. (n = 1), with type strains ATCC 49935T (= W5998T = DSM 44677T), ATCC 49403T (= W5198T = DSM 44676T) ATCC 49404T (= W6705T = DSM 44679T) and ATCC 49938T (= W6743T = DSM 44680T), respectively.},
  doi = {10.1099/ijs.0.02743-0},
  issue = {5},
  pmid = {15388725}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{LamyEtAl2008a,
  year = {2008},
  journal = {Int J Syst Evol Microbiol},
  volume = {58},
  pages = {486-490},
  author = {Lamy, B. and Marchandin, H. and Hamitouche, K. and Laurent, F.},
  title = {\textit{Mycobacterium setense} sp. nov., a \textit{Mycobacterium fortuitum}-group organism isolated from a patient with soft tissue infection and osteitis.},
  abstract = {A Gram-positive, rod-shaped acid-fast bacterium was isolated from a patient with a post-traumatic chronic skin abscess associated with osteitis. Morphological analysis, 16S rRNA, hsp65, sodA and rpoB gene sequence analysis, cell-wall fatty acid and mycolic acid composition analyses and biochemical tests showed that the isolate, designated ABO-M06\textsuperscript{T}, belonged to the genus \textit{Mycobacterium}. Its phenotype was unique and genetic and phylogenetic findings suggest that strain ABO-M06\textsuperscript{T} represents a novel species within the \textit{Mycobacterium fortuitum} group. The name \textit{Mycobacterium setense} sp. nov. is proposed for this novel species, with the type strain ABO-M06\textsuperscript{T} (=CIP 109395\textsuperscript{T}=DSM 45070\textsuperscript{T}).},
  doi = {10.1099/ijs.0.65222-0},
  issue = {2},
  pmid = {18218954}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{BonickeJuhasz1964b,
  year = {1964},
  journal = {Zentralblatt für Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene. Abteilung I},
  volume = {192},
  pages = {133-135},
  author = {Bönicke, R. and Juhasz, S.E.},
  title = {Beschreibung der neuen Species \textit{Mycobacterium vaccae} n. sp.}
}

@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{ThorelEtAl1990a,
  year = {1990},
  journal = {Int J Syst Bacteriol},
  volume = {40},
  pages = {254-260},
  author = {Thorel, M.F. and Krichevsky, M. and Levy-Frebault, V.V.},
  title = {Numerical taxonomy of mycobactin-dependent mycobacteria, emended description of \textit{Mycobacterium avium}, and description of \textit{Mycobacterium avium} subsp. \textit{avium} subsp. nov., \textit{Mycobacterium avium} subsp. \textit{paratuberculosis} subsp. nov., and \textit{Mycobacterium avium} subsp. \textit{silvaticum} subsp. nov.},
  abstract = {We performed a numerical taxonomy analysis of 38 \textit{Mycobacterium paratuberculosis} and related mycobacterial strains, including wood pigeon mycobacteria; this analysis was based on 22 tests, which were selected for their potential discriminative value from a total of 51 tests studied and produced four well-defined clusters. Cluster 1 contained the \textit{M. paratuberculosis} strains, including two strains isolated from Crohn's disease patients; cluster 2 contained \textit{Mycobacterium avium} and \textit{Mycobacterium intracellulare} reference strains; cluster 3 consisted of the wood pigeon mycobacteria; and the only strain in cluster 4 was \textit{M. paratuberculosis} 316F, which is used for antigen and vaccine production. Strains in cluster 1 were mycobactin dependent even when they were subcultured, whereas strains in cluster 3 were unable to grow on egg medium and their growth was stimulated by pH 5.5. Growth stimulation by pyruvate, resistance to D-cycloserine (50 micrograms/ml), and alkaline phosphatase activity also were characteristics that were useful for discriminating between clusters 1 and 3. The results of previous DNA-DNA hybridization studies have demonstrated that \textit{M. avium} Chester 1901, \textit{M. paratuberculosis} Bergey et al. 1923, and the wood pigeon mycobacteria belong to a single genomic species, and we propose that the name of this species should be \textit{M. avium}. On the basis of the results of previous genomic analyses based on restriction fragment length, the results of polymorphism studies, and DNA patterns determined by field inversion gel electrophoresis as well as the results of our phenotypic study, we propose that the species should be divided into subspecies which correspond to pathogenicity and host range characteristics.(ABSTRACT TRUNCATED AT 250 WORDS)},
  doi = {10.1099/00207713-40-3-254},
  issue = {3},
  pmid = {2397193}
}

@article{Wayne1966a,
  year = {1966},
  journal = {Am Rev Respir Dis},
  volume = {93},
  pages = {919-928},
  author = {Wayne, L.G.},
  title = {Classification and identification of mycobacteria. 3. Species within group 3.},
  doi = {10.1164/arrd.1966.93.6.919},
  issue = {6},
  pmid = {5942239}
}

@book{Chester1901a,
  author = {Chester, F.D.},
  year = {1901},
  title = {A Manual of Determinative Bacteriology},
  publisher = {The Macmillan Co.},
  address = {New York}
}


@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{RhodesEtAl2005a,
  year = {2005},
  journal = {Int J Syst Evol Microbiol},
  volume = {55},
  pages = {1139-1147},
  author = {Rhodes, M.W. and Kator, H. and McNabb, A. and Deshayes, C. and Reyrat, J.M. and Brown-Elliott, B.A. and Wallace, R.J. and Trott, K.A. and Parker, J.M. and Lifland, B. and Osterhout, G. and Kaattari, I. and Reece, K. and Vogelbein, W. and Ottinger, C.A.},
  title = {\textit{Mycobacterium pseudoshottsii} sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis).},
  abstract = {A group of slowly growing photochromogenic mycobacteria was isolated from Chesapeake Bay striped bass (Morone saxatilis) during an epizootic of mycobacteriosis. Growth characteristics, acid-fastness and 16S rRNA gene sequencing results were consistent with those of the genus \textit{Mycobacterium}. Biochemical reactions, growth characteristics and mycolic acid profiles (HPLC) resembled those of \textit{Mycobacterium shottsii}, a non-pigmented mycobacterium also isolated during the same epizootic. Sequencing of the 16S rRNA genes, the gene encoding the exported repeated protein (erp) and the gene encoding the 65 kDa heat-shock protein (hsp65) and restriction enzyme analysis of the hsp65 gene demonstrated that this group of isolates is unique. Insertion sequences associated with \textit{Mycobacterium ulcerans}, IS2404 and IS2606, were detected by PCR. These isolates could be differentiated from other slowly growing pigmented mycobacteria by their inability to grow at 37 degrees C, production of niacin and urease, absence of nitrate reductase, negative Tween 80 hydrolysis and resistance to isoniazid (1 mug ml(-1)), p-nitrobenzoic acid, thiacetazone and thiophene-2-carboxylic hydrazide. On the basis of this polyphasic study, it is proposed that these isolates represent a novel species, \textit{Mycobacterium pseudoshottsii} sp. nov. The type strain, L15\textsuperscript{T}, has been deposited in the American Type Culture Collection as ATCC BAA-883\textsuperscript{T} and the National Collection of Type Cultures (UK) as NCTC 13318\textsuperscript{T}.},
  doi = {10.1099/ijs.0.63343-0},
  issue = {3},
  pmid = {15879246}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{SchinskyEtAl2004a,
  year = {2004},
  journal = {Int J Syst Evol Microbiol},
  volume = {54},
  pages = {1653-1667},
  author = {Schinsky, M.F. and Morey, R.E. and Steigerwalt, A.G. and Douglas, M.P. and Wilson, R.W. and Floyd, M.M. and Butler, W.R. and Daneshvar, M.I. and Brown-Elliott, B.A. and Wallace, R.J.J. and McNeil, M.M. and Brenner, D.J. and Brown, J.M.},
  title = {Taxonomic variation in the \textit{Mycobacterium fortuitum} third biovariant complex: description of \textit{Mycobacterium boenickei} sp. nov., \textit{Mycobacterium houstonense} sp. nov., \textit{Mycobacterium neworleansense} sp. nov. and \textit{Mycobacterium brisbanense} sp. nov. and recognition of \textit{Mycobacterium porcinum} from human clinical isolates.},
  abstract = {The \textit{Mycobacterium fortuitum} third biovariant complex (sorbitol-negative and sorbitol-positive) contains unnamed taxa first characterized in 1991. These organisms can cause respiratory infections, a spectrum of soft tissue and skeletal infections, bacteraemia and disseminated disease. To evaluate this group of organisms, clinical reference isolates and the type strains of \textit{M. fortuitum} third biovariant complex sorbitol-negative (n = 21), \textit{M. fortuitum} third biovariant complex sorbitol-positive (n = 3), \textit{M. fortuitum} (n = 3), \textit{Mycobacterium peregrinum} (pipemidic acid-susceptible) (n = 1), \textit{Mycobacterium porcinum} (n = 1), \textit{Mycobacterium senegalense} (n = 2) and \textit{Mycobacterium septicum} (n = 1) were characterized by using conventional phenotypic (morphological, physiological and antimicrobial susceptibilities), chemotaxonomic (HPLC and cellular fatty acids) and genotypic [RFLP of the rRNA gene (ribotyping), PCR-RFLP of a 439 bp segment of the 65 kDa hsp gene (PCR restriction analysis) and 16S rRNA gene sequence] analysis, DNA G + C content and DNA-DNA relatedness analyses. The results of these studies indicated that the strains comprised \textit{M. porcinum} (n = 13), \textit{M. septicum} (n = 1) and four novel closely related genetic groups within the \textit{M. fortuitum} third biovariant complex: \textit{Mycobacterium boenickei} sp. nov. (n = 6), \textit{Mycobacterium houstonense} sp. nov. (n = 2), \textit{Mycobacterium neworleansense} sp. nov. (n = 1) and \textit{Mycobacterium brisbanense} sp. nov. (n = 1), with type strains ATCC 49935T (= W5998T = DSM 44677T), ATCC 49403T (= W5198T = DSM 44676T) ATCC 49404T (= W6705T = DSM 44679T) and ATCC 49938T (= W6743T = DSM 44680T), respectively.},
  doi = {10.1099/ijs.0.02743-0},
  issue = {5},
  pmid = {15388725}
}


@article{GuptaEtAl2018a,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {67},
  author = {Gupta, R.S. and Lo, B. and Son, J.},
  title = {Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus \textit{Mycobacterium} into an Emended Genus \textit{Mycobacterium} and Four Novel Genera.},
  abstract = {The genus \textit{Mycobacterium} contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of \textit{Mycobacterium} species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus \textit{Mycobacterium}, 136 core proteins for the phylum \textit{Actinobacteria} and 8 other conserved proteins. Additionally, the overall genome similarity amongst the \textit{Mycobacterium} species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus \textit{Mycobacterium} at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all \textit{Mycobacterium} species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus \textit{Mycobacterium} and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus \textit{Mycobacterium} into an emended genus \textit{Mycobacterium} encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. \textit{Mycolicibacterium} gen. nov., \textit{Mycolicibacter} gen. nov., \textit{Mycolicibacillus} gen. nov. and \textit{Mycobacteroides} gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.},
  doi = {10.3389/fmicb.2018.00067},
  pmid = {29497402}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}

@article{SchinskyEtAl2000b,
  year = {2000},
  journal = {Int J Syst Evol Microbiol},
  volume = {50},
  pages = {575-581},
  author = {Schinsky, M.F. and McNeil, M.M. and Whitney, A.M. and Steigerwalt, A.G. and Lasker, B.A. and Floyd, M.M. and Hogg, G.G. and Brenner, D.J. and Brown, J.M.},
  title = {\textit{Mycobacterium septicum} sp. nov., a new rapidly growing species associated with catheter-related bacteraemia.},
  abstract = {Rapidly growing mycobacteria are capable of causing several clinical diseases in both immunosuppressed and immunocompetent individuals. A previously unidentified, rapidly growing mycobacterium was determined to be the causative agent of central line sepsis in a child with underlying metastatic hepatoblastoma. Four isolates of this mycobacterium, three from blood and one from the central venous catheter tip, were studied. Phenotypic characterization, HPLC and genetic analysis revealed that while this organism most closely resembled members of the \textit{Mycobacterium fortuitum} complex and \textit{Mycobacterium senegalense}, it differed from all previously described species. Phenotypic tests useful in differentiating this species from similar rapidly growing mycobacteria included: growth at 42 degrees C, hydrolysis of acetamide, utilization of citrate, production of arylsulfatase (3-d), acidification of D-mannitol and i-myo-inositol, and susceptibility to erythromycin, vancomycin and tobramycin. The name \textit{Mycobacterium septicum} is proposed for this new species. The type strain has been deposited in Deutsche Sammlung von Mikroorganismen und Zellkulturen as DSM 44393T and in the American Type Culture Collection as strain ATCC 700731T.},
  doi = {10.1099/00207713-50-2-575},
  issue = {2},
  pmid = {10758863}
}


@article{BrownelliottEtAl2018a,
  year = {2018},
  journal = {Int J Syst Evol Microbiol},
  volume = {68},
  pages = {3557-3562},
  author = {Brown-Elliott, B.A. and Simmer, P.J. and Trovato, A. and Hyle, E.P. and Droz, S. and Buckwalter, S.P. and Borroni, E. and Branda, J.A. and Iana, E. and Mariottini, A. and Nelson, J. and Matteelli, A. and Toney, N.C. and Scarparo, C. and de Man, T.J.B. and Vasireddy, R. and Gandhi, R.T. and Wengenack, N.L. and Cirillo, D.M. and Wallace, R.J. and Tortoli, E.},
  title = {\textit{Mycobacterium decipiens} sp. nov., a new species closely related to the \textit{Mycobacterium tuberculosis} complex.},
  abstract = {Two mycobacterial strains with close similarity to the \textit{Mycobacterium tuberculosis} complex (MTBC) were isolated from cutaneous lesions of patients in the USA and Italy. At the phenotypic level, similarities to the MTBC included slow growth rate, rough morphotype of the unpigmented colonies and nearly identical high-performance liquid chromatography profiles of mycolic acids. In contrast to the MTBC, the strains were niacin- and nitrate-negative, and catalase-positive both at 68 degrees C and in semi-quantitative tests. The clinical isolates were more closely related to \textit{M. tuberculosis} than to any other known mycobacterium and scored positive with commercial DNA probes (Hologic AccuProbe \textit{M. tuberculosis}). Both average nucleotide identity and genome-to-genome distance suggested the strains are different from the MTBC. Therefore, given the distinguishing phenotypic and genomic-scale differences, we submit that the strains belong to a new species we have named Mycobacteriumdecipiens with type strain TBL 1200985\textsuperscript{T} (=ATCC TSD-117\textsuperscript{T}=DSM 105360\textsuperscript{T}).},
  doi = {10.1099/ijsem.0.003031},
  issue = {11},
  pmid = {30204586}
}


@article{CastejonEtAl2018a,
  year = {2018},
  journal = {Int J Syst Evol Microbiol},
  volume = {68},
  pages = {1998-2005},
  author = {Castejon, M. and Menendez, M.C. and Comas, I. and Vicente, A. and Garcia, M.J.},
  title = {Whole-genome sequence analysis of the \textit{Mycobacterium avium} complex and proposal of the transfer of \textit{Mycobacterium yongonense} to \textit{Mycobacterium intracellulare} subsp. \textit{yongonense} subsp. nov.},
  abstract = {Bacterial whole-genome sequences contain informative features of their evolutionary pathways. Comparison of whole-genome sequences have become the method of choice for classification of prokaryotes, thus allowing the identification of bacteria from an evolutionary perspective, and providing data to resolve some current controversies. Currently, controversy exists about the assignment of members of the \textit{Mycobacterium avium} complex, as is for the cases of \textit{Mycobacterium yongonense} and '\textit{Mycobacterium} indicus pranii'. These two mycobacteria, closely related to \textit{Mycobacterium intracellulare} on the basis of standard phenotypic and single gene-sequences comparisons, were not considered a member of such species on the basis on some particular differences displayed by a single strain. Whole-genome sequence comparison procedures, namely the average nucleotide identity and the genome distance, showed that those two mycobacteria should be considered members of the species \textit{M. intracellulare}. The results were confirmed with other whole-genome comparison supplementary methods. According to the data provided, \textit{Mycobacterium yongonense} and '\textit{Mycobacterium} indicus pranii' should be considered and renamed and included as members of \textit{M. intracellulare}. This study highlights the problems caused when a novel species is accepted on the basis of a single strain, as was the case for \textit{M. yongonense}. Based mainly on whole-genome sequence analysis, we conclude that \textit{M. yongonense} should be reclassified as a subspecies of \textit{Mycobacterium} intracellulareas \textit{Mycobacterium} intracellularesubsp. yongonense and '\textit{Mycobacterium} indicus pranii' classified in the same subspecies as the type strain of \textit{Mycobacterium intracellulare} and classified as \textit{Mycobacterium} intracellularesubsp. intracellulare.},
  doi = {10.1099/ijsem.0.002767},
  issue = {6},
  pmid = {29683417}
}

@article{KimEtAl2013a,
  year = {2013},
  journal = {Int J Syst Evol Microbiol},
  volume = {63},
  pages = {192-199},
  author = {Kim, B.J. and Math, R.K. and Jeon, C.O. and Yu, H.K. and Park, Y.G. and Kook, Y.H. and Kim, B.J.},
  title = {\textit{Mycobacterium yongonense} sp. nov., a slow-growing non-chromogenic species closely related to \textit{Mycobacterium intracellulare}.},
  abstract = {A slow-growing non-chromogenic mycobacterium was isolated from a patient with pulmonary disease. Phenotypically, strain 05-1390\textsuperscript{T} was similar to \textit{Mycobacterium intracellulare} ATCC 13950\textsuperscript{T}. The 16S rRNA gene sequence (1385 bp) of strain 05-1390\textsuperscript{T} showed a high degree of similarity to those of the \textit{M. intracellulare} complex, namely \textit{Mycobacterium marseillense} 5351974\textsuperscript{T} (100 %), \textit{M. intracellulare} ATCC 13950\textsuperscript{T} (99.8 %) and \textit{Mycobacterium chimaera} DSM 44623\textsuperscript{T} (99.9 %). Phylogenetic analysis based on internal transcribed spacer 1 (ITS1) and the hsp65 gene indicated that strain 05-1390\textsuperscript{T} was closely related to \textit{M. intracellulare} ATCC 13950\textsuperscript{T}, but that it was a distinct phylogenetic entity. Of particular interest, an analysis based on the rpoB gene (701 bp) showed that it is closely related to \textit{Mycobacterium parascrofulaceum} ATCC BAA-614\textsuperscript{T} (99.4 %), a scotochromogenic strain, rather than to the \textit{M. intracellulare}-related strains. Unique MALDI-TOF MS profiles also supported the taxonomic status of this strain as a distinct species. These data support the conclusion that strain 05-1390\textsuperscript{T} represents a novel mycobacterial species, for which the name \textit{Mycobacterium yongonense} sp. nov. is proposed; the type strain is 05-1390\textsuperscript{T} ( = DSM 45126\textsuperscript{T} = KCTC 19555\textsuperscript{T}).},
  doi = {10.1099/ijs.0.037465-0},
  issue = {1},
  pmid = {22427442}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{MurciaEtAl2006a,
  year = {2006},
  journal = {Int J Syst Evol Microbiol},
  volume = {56},
  pages = {2049-2054},
  author = {Murcia, M.I. and Tortoli, E. and Menendez, M.C. and Palenque, E. and Garcia, M.J.},
  title = {\textit{Mycobacterium colombiense} sp. nov., a novel member of the \textit{Mycobacterium avium} complex and description of MAC-X as a new ITS genetic variant.},
  abstract = {Forty-five mycobacterial strains isolated from 23 Colombian HIV-positive patients were identified as members of the \textit{Mycobacterium avium} complex (MAC) and were characterized using different molecular approaches. Seven of the isolates showed characteristic features that allowed them to be differentiated from other members of the complex. The isolates had a novel 16S-23S rRNA internal transcribed spacer (ITS 1) gene sequence which is described as a new sequevar, MAC-X. All of the seven novel isolates gave a positive result with the MAC-specific AccuProbe (Gen-Probe), but tested negative for \textit{Mycobacterium avium} and \textit{Mycobacterium intracellulare} species-specific probes (64 and 100 % of the isolates, respectively). The novel isolates could be differentiated phenotypically from other members of the MAC on the basis of the production of urease and by a consistent mycolic acid pattern. The novel isolates shared some characteristics with \textit{M. avium}, such as the avium variant I (av-I) pattern of the hsp65 gene as determined by PCR restriction analysis and a positive PCR result for the mig (macrophage-induced) gene. However, the novel isolates showed a unique 16S rRNA gene sequence. DNA-DNA relatedness values, from 24 to 44 %, confirmed the distinction of the novel isolates from other members of the MAC at the genetic level and their status as members of a separate species. The novel isolates are proposed as representatives of a novel species, \textit{Mycobacterium colombiense} sp. nov., that is closely related to \textit{M. avium} within the MAC. The type strain is 10B\textsuperscript{T} (=CIP 108962\textsuperscript{T}=CECT 3035\textsuperscript{T}).},
  doi = {10.1099/ijs.0.64190-0},
  issue = {9},
  pmid = {16957098}
}

@article{NouiouiEtAl2018c,
  year = {2018},
  journal = {Front Microbiol},
  volume = {9},
  pages = {2007},
  author = {Nouioui, I. and Carro, L. and Garcia-Lopez, M. and Meier-Kolthoff, J.P. and Woyke, T. and Kyrpides, N.C. and Pukall, R. and Klenk, H.P. and Goodfellow, M. and Goker, M.},
  title = {Genome-Based Taxonomic Classification of the Phylum \textit{Actinobacteria}.},
  abstract = {The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum \textit{Actinobacteria} but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.},
  doi = {10.3389/fmicb.2018.02007},
  pmid = {30186281}
}


@article{TaginiEtAl2019a,
  year = {2019},
  journal = {Int J Syst Evol Microbiol},
  volume = {69},
  pages = {1696-1704},
  author = {Tagini, F. and Aeby, S. and Bertelli, C. and Droz, S. and Casanova, C. and Prod'hom, G. and Jaton, K. and Greub, G.},
  title = {Phylogenomics reveal that \textit{Mycobacterium kansasii} subtypes are species-level lineages. Description of \textit{Mycobacterium pseudokansasii} sp. nov., \textit{Mycobacterium innocens} sp. nov. and \textit{Mycobacterium attenuatum} sp. nov.},
  abstract = {Among the species \textit{Mycobacterium kansasii}, seven subtypes have been previously reported based on the PCR and the restriction fragment length polymorphism of the gene hsp65. Here, we used whole-genome sequencing to refine \textit{M. kansasii} taxonomy and correct multiple inconsistencies. Average nucleotide identity (ANI) values between \textit{M. kansasii} subtypes ranged from 88.4 to 94.2 %, lower than the accepted 95-96 % cut-off for species delineation. In addition, \textit{Mycobacterium gastri} was closer to the \textit{M. kansasii} subtypes 1, 2, 3, 4 and 5 than \textit{M. kansasii} subtype 6. The recently described species \textit{Mycobacterium persicum} shared 99.77 % ANI with \textit{M. kansasii} subtype 2. Consistent with the ANI results, the digital DNA-DNA hybridization value was below the 70 % threshold for species delineation between subtypes and above it within subtypes as well as between subtype 2 and \textit{M. persicum}. Furthermore, core-genome phylogeny confirmed the current \textit{M. kansasii} species to be polyphyletic. Hence, we propose (i) \textit{Mycobacterium pseudokansasii} sp. nov., replacing subtype 3, with the type strain MK142\textsuperscript{T}(=CCUG 72128\textsuperscript{T}=DSM 107152\textsuperscript{T}), (ii) \textit{Mycobacterium innocens} sp. nov., replacing subtype 5, with the type strain MK13\textsuperscript{T} (=CCUG 72126\textsuperscript{T}=DSM 107161\textsuperscript{T}), and (iii) \textit{Mycobacterium attenuatum} sp. nov., replacing subtype 6, with the type strain MK41\textsuperscript{T}(=CCUG 72127\textsuperscript{T}=DSM 107153\textsuperscript{T}). Subtype 4 represents a new species-level lineage based on the genomic data but no strain was available. No genome sequence or strain was available for subtype 7. The proposed nomenclature will facilitate the identification of the most pathogenic subtype 1 as \textit{M. kansasii} by clinicians while the new species names suggest the attenuated pathogenicity of the other subtypes.},
  doi = {10.1099/ijsem.0.003378},
  issue = {6},
  pmid = {30950782}
}


@article{PourahmadEtAl2015a,
  year = {2015},
  journal = {Int J Syst Evol Microbiol},
  volume = {65},
  pages = {4724-4729},
  author = {Pourahmad, F. and Pate, M. and Ocepek, M. and Borroni, E. and Cabibbe, A.M. and Capitolo, E. and Cittaro, D. and Frizzera, E. and Jencic, V. and Mariottini, A. and Marumo, K. and Vaggelli, G. and Cirillo, D.M. and Tortoli, E.},
  title = {\textit{Mycobacterium angelicum} sp. nov., a non-chromogenic, slow-growing species isolated from fish and related to \textit{Mycobacterium szulgai}.},
  abstract = {The name '\textit{Mycobacterium angelicum}' dates back to 2003 when it was suggested for a slowly growing mycobacterium isolated from freshwater angelfish. This name is revived here and the novel species is proposed on the basis of the polyphasic characterization of four strains including the original one. The four strains presented 100 % 16S rRNA gene sequence similarity with \textit{Mycobacterium szulgai} but clearly differed from \textit{M. szulgai} for the milky white aspect of the colonies. The sequence similarity with the type strain of \textit{M. szulgai} ranged, in eight additionally investigated genetic targets, from 78.9 to 94.3 %, an evident contrast with the close relatedness that emerged at the level of 16S rRNA gene. The average nucleotide identity between the genomes of \textit{M. szulgai} DSM 44166T and strain 126/5/03T (type strain of the novel species) was 92.92 %, and supported the status of independent species. The confirmation of the name \textit{Mycobacterium angelicum} sp. nov. is proposed, with strain 126/5/03T ( = CIP 109313T = DSM 45057T) as the type strain.},
  doi = {10.1099/ijsem.0.000642},
  issue = {12},
  pmid = {26420689}
}