List of new names and new combinations previously effectively, but not validly, published

Oren, Aharon

doi:10.1099/ijsem.0.002711

Cited by 167 publications

(16 citation statements)

References 12 publications

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“…The article by GUPTA et al [1] is indeed validly published (it contains the protologue for all the species taken into account, where the respective type strains are confirmed) and the new names have been included in a validation list by IJSEM [5]. As a consequence, the species allocated in genera other than Mycobacterium (Mycobacteroides, Mycolicibacter, Mycolicibacterium and Mycolicibacillus) have synonyms, both of which can correctly be used.…”

Section: @Erspublicationsmentioning

confidence: 99%

“…What has caused most confusion among mycobacteriologists was not the study by GUPTA et al [1], but the validation of the novel nomenclature [5] published by the International Journal of Systematic and Evolutionary Microbiology (IJSEM), the official publication of the International Committee on Systematics of Prokaryotes. We believe the new nomenclature has the potential to cause confusion and provides no benefits to the field of clinical mycobacteriology.…”

Section: @Erspublicationsmentioning

confidence: 99%

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Same meat, different gravy: ignore the new names of mycobacteria

et al. 2019

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@ERSpublicationsA new name for most Mycobacterium species has been recently proposed. According to taxonomic rules novel and previous nomenclature coexist and are synonyms. The use of the latter has the advantage of avoiding confusion for healthcare and harm for patients. http://bit.ly/2XhTACc Cite this article as: Tortoli E, Brown-Elliott BA, Chalmers JD, et al. Same meat, different gravy: ignore the new names of mycobacteria. Eur Respir J 2019; 54: 1900795 [https://doi.org/10.1183/13993003.00795-2019].In a recent article, GUPTA et al. [1] have proposed a revision of the taxonomy of mycobacteria with the redistribution of 150 species of the genus Mycobacterium into five different genera; the four newly proposed genera hosting the nontuberculous mycobacteria (NTM) are called Mycobacteroides, Mycolicibacter, Mycolicibacterium and Mycolicibacillus. The proposed taxonomy is based on the theory of synapomorphies, molecular markers that most likely appeared early in an ancestor and then were vertically

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Section: @Erspublicationsmentioning

confidence: 99%

Section: @Erspublicationsmentioning

confidence: 99%

Same meat, different gravy: ignore the new names of mycobacteria

et al. 2019

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“…The dendrogram computed with the distance matrix of pairwise ANI values showed two separated groups (Figure 6). One group represents the clade of slow-growing mycobacteria designated as "Tuberculosis-Simiae" and depicts the emended genus Mycobacterium (Gupta et al, 2018;Oren and Garrity, 2018). This group includes well-known human pathogens (Gupta et al, 2018), most notably Mycobacterium leprae and Mycobacterium tuberculosis, causative agents of leprosy and tuberculosis, respectively (Magee and Ward, 2012;Lory, 2014).…”

Section: Genomic Features Ani and Phylogeny Of Sequenced Strainsmentioning

confidence: 99%

“…This group includes well-known human pathogens (Gupta et al, 2018), most notably Mycobacterium leprae and Mycobacterium tuberculosis, causative agents of leprosy and tuberculosis, respectively (Magee and Ward, 2012;Lory, 2014). The second group, in which the four sequenced bacteria are included, encompasses species from the clade "Fortuitum-Vaccae," recently transferred to a new genus, Mycolicibacterium gen. nov. (Oren and Garrity, 2018).…”

Section: Genomic Features Ani and Phylogeny Of Sequenced Strainsmentioning

confidence: 99%

Beneficial Endophytic Bacteria-Serendipita indica Interaction for Crop Enhancement and Resistance to Phytopathogens

et al. 2019

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Serendipita (=Piriformospora) indica is a fungal endophytic symbiont with the capabilities to enhance plant growth and confer resistance to different stresses. However, the application of this fungus in the field has led to inconsistent results, perhaps due to antagonism with other microbes. Here, we studied the impact of individual bacterial isolates from the endophytic bacterial community on the in vitro growth of S. indica. We further analyzed how combinations of bacteria and S. indica influence plant growth and protection against the phytopathogens Fusarium oxysporum and Rhizoctonia solani. Bacterial strains of the genera Bacillus, Enterobacter and Burkholderia negatively affected S. indica growth on plates, whereas Mycolicibacterium, Rhizobium, Paenibacillus strains and several other bacteria from different taxa stimulated fungal growth. To further explore the potential of bacteria positively interacting with S. indica, four of the most promising strains belonging to the genus Mycolicibacterium were selected for further experiments. Some dual inoculations of S. indica and Mycolicibacterium strains boosted the beneficial effects triggered by S. indica, further enhancing the growth of tomato plants, and alleviating the symptoms caused by the phytopathogens F. oxysporum and R. solani. However, some combinations of S. indica and bacteria were less effective than individual inoculations. By analyzing the genomes of the Mycolicibacterium strains, we revealed that these bacteria encode several genes predicted to be involved in the stimulation of S. indica growth, plant development and tolerance to abiotic and biotic stresses. Particularly, a high number of genes related to vitamin and nitrogen metabolism were detected. Taking into consideration multiple interactions on and inside plants, we showed in this study that some bacterial strains may induce beneficial effects on S. indica and could have an outstanding influence on the plant-fungus symbiosis.

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“…Mycolicibacterium smegmatis is a rapid-growing bacterium and previously belonged to the genus Mycobacterium as basonym Mycobacterium smegmatis , to which many pathogenic mycobacteria, including M. tuberculosis , a causative agent of tuberculosis, and M. leprae , a causative agent of leprosy, are belonging (Gupta et al, 2018 ; Oren and Garrity, 2018 ). Therefore, M. smegmatis has been quite often used as substitute for M. tuberculosis or M. leprae in studies, especially in the field of molecular biology, and there are a number of literature (Bashiri and Baker, 2015 ; Brown-Elliott and Philley, 2017 ), more than 15 papers, listed only in 2018 (Angara et al, 2018 ; Burian and Thompson, 2018 ; Chandran et al, 2018 ; Chen et al, 2018 ; Dal Molin et al, 2018 ; Ghosh et al, 2018 ; Goins et al, 2018 ; Jesus et al, 2018 ; Kaur et al, 2018 ; Kumar et al, 2018 ; Lopez et al, 2018 ; Marney et al, 2018 ; Mortuza et al, 2018 ; Richards et al, 2018 ; Singh et al, 2018 ; Tsaloglou et al, 2018 ; Verma et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Mycolicibacterium smegmatis, Basonym Mycobacterium smegmatis, Expresses Morphological Phenotypes Much More Similar to Escherichia coli Than Mycobacterium tuberculosis in Quantitative Structome Analysis and CryoTEM Examination

et al. 2018

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A series of structome analyses, that is, quantitative and three-dimensional structural analysis of a whole cell at the electron microscopic level, have already been achieved individually in Exophiala dermatitidis, Saccharomyces cerevisiae, Mycobacterium tuberculosis, Myojin spiral bacteria, and Escherichia coli. In these analyses, sample cells were processed through cryo-fixation and rapid freeze-substitution, resulting in the exquisite preservation of ultrastructures on the serial ultrathin sections examined by transmission electron microscopy. In this paper, structome analysis of non pathogenic Mycolicibacterium smegmatis, basonym Mycobacterium smegmatis, was performed. As M. smegmatis has often been used in molecular biological experiments and experimental tuberculosis as a substitute of highly pathogenic M. tuberculosis, it has been a task to compare two species in the same genus, Mycobacterium, by structome analysis. Seven M. smegmatis cells cut into serial ultrathin sections, and, totally, 220 serial ultrathin sections were examined by transmission electron microscopy. Cell profiles were measured, including cell length, diameter of cell and cytoplasm, surface area of outer membrane and plasma membrane, volume of whole cell, periplasm, and cytoplasm, and total ribosome number and density per 0.1 fl cytoplasm. These data are based on direct measurement and enumeration of exquisitely preserved single cell structures in the transmission electron microscopy images, and are not based on the calculation or assumptions from biochemical or molecular biological indirect data. All measurements in M. smegmatis, except cell length, are significantly higher than those of M. tuberculosis. In addition, these data may explain the more rapid growth of M. smegmatis than M. tuberculosis and contribute to the understanding of their structural properties, which are substantially different from M. tuberculosis, relating to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance in relation to the ratio of the targets to the corresponding drugs. In addition, data obtained from cryo-transmission electron microscopy examination were used to support the validity of structome analysis. Finally, our data strongly support the most recent establishment of the novel genus Mycolicibacterium, into which basonym Mycobacterium smegmatis has been classified.

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List of new names and new combinations previously effectively, but not validly, published

Cited by 167 publications

References 12 publications

Same meat, different gravy: ignore the new names of mycobacteria

Same meat, different gravy: ignore the new names of mycobacteria

Beneficial Endophytic Bacteria-Serendipita indica Interaction for Crop Enhancement and Resistance to Phytopathogens

Mycolicibacterium smegmatis, Basonym Mycobacterium smegmatis, Expresses Morphological Phenotypes Much More Similar to Escherichia coli Than Mycobacterium tuberculosis in Quantitative Structome Analysis and CryoTEM Examination

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