Necessity and rationale for the proposed name changes in the classification of Mollicutes species. Reply to: ‘Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein’, by M. Balish et al. (Int J Syst Evol Microbiol, 2019;69:3650–3653)
This response summarizes the highly disordered state of the Mollicutes taxonomy that existed until recently, where most Mollicutes taxa lacked proper circumscriptions and their names were not in accordance with the International Code of Nomenclature of Prokaryotes and illegitimate. We also summarize the comprehensive phylogenomic and comparative genomic studies forming the basis for the proposed changes in the classification of Mollicultes species. Our responses to the concerns raised by Balish et al., show that the proposed taxonomic changes do not violate any essential point of the Code. Instead the proposed name changes rectify numerous taxonomic anomalies that have long plagued the classification of Mollicutes species, leading to a better understanding of their evolutionary relationships and bringing their nomenclature in conformity with the Code.
BalishM,
BertacciniA,
BlanchardA,
BrownD,
BrowningG et al. Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein. Int J Syst Evol Microbiol2019; 69:3650-3653 [View Article]
GuptaRS,
SonJ,
OrenA.
A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera. Antonie van Leeuwenhoek2019; 112:561–588 [View Article]
GuptaRS,
SawnaniS,
AdeoluM,
AlnajarS,
OrenA.
Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera. Antonie van Leeuwenhoek2018; 111:1583–1630 [View Article]
MayM,
BalishMF,
BlanchardA.
The Order Mycoplasmatales
. In
RosenbergE,
DeLongEF,
LoryS,
StackebrandtE,
ThompsonF.
(editors) The Prokaryotes. Firmicutes and Tenericutes Berlin: Springer; 2014 pp 515–550
GasparichGE.
The Family Entomoplasmataceae
. In
RosenbergE,
DeLongEF,
LoryS,
StackebrandtE,
ThompsonF.
(editors) The Prokaryotes. Firmicutes and Tenericutes Berlin: Springer; 2014 pp 505–514
WeisburgWG,
TullyJG,
RoseDL,
PetzelJP,
OyaizuH et al. A phylogenetic analysis of the mycoplasmas: basis for their classification. J Bacteriol1989; 171:6455–6467 [View Article]
TullyJG,
BovéJM,
LaigretF,
WhitcombRF.
Revised taxonomy of the class Mollicutes: proposed elevation of a monophyletic cluster of arthropod-associated Mollicutes to ordinal rank (Entomoplasmatales ord. nov.), with provision for familial rank to separate species with nonhelical morphology (Entomoplasmataceae fam. nov.) from helical species (Spiroplasmataceae), and emended descriptions of the order Mycoplasmatales, family Mycoplasmataceae
. Int J Syst Evol Microbiol1993; 43:378–385
FreundtEA.
The classification of the pleuropneumonia group of organisms (Borrelomycetales). International Bulletin of Bacteriological Nomenclature and Taxonomy1955; 5:67–78 [View Article]
FirraoG,
BrownDR.
International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of Mollicutes: Minutes of the meetings, 11 and 16 July 2010, Chianciano Terme, Italy. Int J Syst Evol Microbiol2011; 61:695–697
GuptaRS.
Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification. FEMS Microbiol Rev2016; 40:520–553 [View Article]
BarbourAG,
AdeoluM,
GuptaRS.
Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos, et al. (2016) there is inadequate evidence to support the division of the genus Borrelia
. Int J Syst Evol Microbiol2017; 67:2058–2067 [View Article]
GuptaRS,
NaushadS,
BakerS.
Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol2015; 65:1050–1069 [View Article]
ParksDH,
ChuvochinaM,
WaiteDW,
RinkeC,
SkarshewskiA et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol2018; 36:996–1004 [View Article]
OrenA,
GarrityGM.
Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie van Leeuwenhoek2014; 106:43–56 [View Article]
GarrityGM,
HoltJG.
The road map to the manual. In
BooneDR,
CastenholzRW.
(editors) Bergey's Manual of Systematic Bacteriology. The Archaea and the Deeply Branching and Phototrophic Bacteria1, 2nd ed. New York: Springer; 2001 pp 119–166
Necessity and rationale for the proposed name changes in the classification of Mollicutes species. Reply to: ‘Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein’, by M. Balish et al. (Int J Syst Evol Microbiol, 2019;69:3650–3653)