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

  • Radhey S. Gupta
  • Sahil Sawnani
  • Mobolaji Adeolu
  • Seema Alnajar
  • Aharon Oren
Original Paper


The genus Mycoplasma, including species earlier classified in the genera Eperythrozoon and Haemobartonella, contains ~ 120 species and constitutes an extensively polyphyletic assemblage of bacteria within the phylum Tenericutes. Due to their small genome sizes and lack of unique characteristics, the relationships among the mycoplasmas/Tenericutes are not reliably discerned. Using genome sequences for 140 Tenericutes, their evolutionary relationships were examined using multiple independent approaches. Phylogenomic trees were constructed for 63 conserved proteins, 45 ribosomal proteins, three main subunits of RNA polymerase and 16S rRNA gene sequences. In all of these trees, Tenericutes species reliably grouped into four main clades designated as the “Acholeplasma”, “Spiroplasma”, “Pneumoniae” and “Hominis” clusters. These clades are also distinguished based on a similarity matrix constructed based on 16S rRNA gene sequences. Mycoplasma species were dispersed across 3 of these 4 clades highlighting their extensive polyphyly. In parallel, our comparative genomic analyses have identified > 100 conserved signature indels (CSIs) and 14 conserved signature proteins (CSPs), which are uniquely shared by the members of four identified clades, strongly supporting their monophyly and identifying them in molecular terms. Mycoplasma mycoides, the type species of the genus Mycoplasma, and a small number of other Mycoplasma species, formed a strongly supported clade within the “Spiroplasma” cluster. Nine CSIs and 14 CSPs reliably distinguish this clade from all other Mycoplasmatales species. The remainder of the Mycoplasmatales species are part of the “Pneumoniae” and “Hominis” clusters, which group together in phylogenetic trees. Here we are proposing that the order Mycoplasmatales should be emended to encompass only the Mycoplasma species within the “Spiroplasma” cluster and that a new order, Mycoplasmoidales ord. nov., should be created to encompass the other Mycoplasma species. The “Pneumoniae” and the “Hominis” clusters are proposed as two new families, Mycoplasmoidaceae fam. nov., which includes the genera Eperythrozoon, Ureaplasma, and the newly proposed genera Malacoplasma and Mycoplasmoides, and Metamycoplasmataceae fam. nov. to contain the newly proposed genera Metamycoplasma, Mycoplasmopsis, and Mesomycoplasma. The results presented here allow reliable discernment, both in phylogenetic and molecular terms, of the members of the two proposed families as well as different described genera within these families including members of the genus Eperythrozoon, which is comprised of uncultivable organisms. The taxonomic reclassifications proposed here, which more accurately portray the genetic diversity among the Tenericutes/Mycoplasma species, provide a new framework for understanding the biological and clinical aspects of these important microbes.


Tenericutes Order Mycoplasmatales Mycoplasma Eperythrozoon Haemobartonella Phylogeny Taxonomy Conserved signature indels Phylogenomic studies Comparative genomics Molecular signatures 



We thank Judy Tran, Talha Tahir, Jeen Son and Joseph Manalo for assistance in the identification and formatting of some of the described CSIs and CSPs. We also thank the editor Dr. Iain Sutcliffe for many helpful suggestions concerning the work presented here. This work was supported by Research Grant No. 249924 from the Natural Science and Engineering Research Council of Canada awarded to Radhey S. Gupta.

Conflict of interest

All of the authors declare that they have no conflict of interest.

Supplementary material

10482_2018_1047_MOESM1_ESM.pdf (3 mb)
Supplementary material 1 (PDF 3107 kb)


  1. Adeolu M, Alnajar S, Naushad S, Gupta RS (2016) Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 66:5575–5599PubMedCrossRefGoogle Scholar
  2. Adler S, Ellenbogen V (1934) A note on two blood parasites of cattle, Eperythrozoon and Bartonella. J Comp Path 47:219–221CrossRefGoogle Scholar
  3. Ahmod NZ, Gupta RS, Shah HN (2011) Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group. J Microbiol Meth 87:278–285CrossRefGoogle Scholar
  4. Allam NM, Lemcke RM (1975) Mycoplasmas isolated from the respiratory tract of horses. Epidemiol Infect 74:385–408Google Scholar
  5. Alnajar S, Gupta RS (2017) Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family. Infect Genet Evol 54:108–127PubMedCrossRefGoogle Scholar
  6. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389–3402PubMedPubMedCentralCrossRefGoogle Scholar
  7. Antunes A (2014) The family Haloplasmataceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Firmicutes and Tenericutes. Springer, Berlin, pp 179–184Google Scholar
  8. Antunes A, Rainey FA, Wanner G, Taborda M, Patzold J, Nobre MF, da Costa MS, Huber R (2008) A new lineage of halophilic, wall-less, contractile bacteria from a brine-filled deep of the Red Sea. J Bacteriol 190:3580–3587PubMedPubMedCentralCrossRefGoogle Scholar
  9. Askaa G, Ernø H (1976) Elevation of Mycoplasma agalactiae subsp. bovis to species rank: Mycoplasma bovis (Hale et al.) comb. nov. Int J Syst Bacteriol 26:323–325CrossRefGoogle Scholar
  10. Barbour AG, Adeolu M, Gupta RS (2017) 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 Microbiol 67:2058–2067PubMedCrossRefGoogle Scholar
  11. Barile MF, Del Giudice RA, Carski TR, Gibbs CJ, Morris JA (1968) Isolation and characterization of Mycoplasma arginini: spec. nov. Proc Soc Exp Biol Med 129:489–494PubMedCrossRefGoogle Scholar
  12. Barile MF, Del Giudice RA, Tully JG (1972) Isolation and characterization of Mycoplasma conjunctivae sp. n. from sheep and goats with keratoconjunctivitis. Infect Immun 5:70–76PubMedPubMedCentralGoogle Scholar
  13. Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET (2017) Genome data provides high support for generic boundaries in Burkholderia sensu lato. Front Microbiol 8:1154PubMedPubMedCentralCrossRefGoogle Scholar
  14. Bhandari V, Gupta RS (2014) Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie van Leeuwenhoek 105:143–168PubMedCrossRefGoogle Scholar
  15. Blackwood KS, Turenne CY, Harmsen D, Kabani AM (2004) Reassessment of sequence-based targets for identification of Bacillus species. J Clin Microbiol 42:1626–1630PubMedPubMedCentralCrossRefGoogle Scholar
  16. Borrel A, Dujardin-Beaumetz E, Jeantet Jouan C (1910) Le microbe de la péripneumonie. Ann Inst Pasteur 24:168–179Google Scholar
  17. Bradbury JM, Forrest M (1984) Mycoplasma cloacale, a new species isolated from a turkey. Int J Syst Bacteriol 34:389–392CrossRefGoogle Scholar
  18. Bradbury JM, Forrest M, Williams A (1983) Mycoplasma lipofaciens, a new species of avian origin. Int J Syst Bacteriol 33:329–335CrossRefGoogle Scholar
  19. Bradbury JM, Jordan FTW, Shimizu T, Stipkovits L, Varga Z (1988) Mycoplasma anseris sp. nov. found in geese. Int J Syst Bacteriol 38:74–76CrossRefGoogle Scholar
  20. Bradbury JM, Abdul-Wahab OMS, Yavari CA, Dupiellet JP, Bové JM (1993) Mycoplasma imitans sp. nov. is related to Mycoplasma gallisepticum and found in birds. Int J Syst Bacteriol 43:721–728PubMedCrossRefGoogle Scholar
  21. Brown DR (2010) Phylum XVI. Tenericutes Murray 1984a, 356VP (Effective Publication: Murray 1985b, 33). In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 4. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. Springer, New York, pp 567–568CrossRefGoogle Scholar
  22. Brown DR, Farley JM, Zacher LA, Carlton JM, Clippinger TL, Tully JG, Brown MB (2001a) Mycoplasma alligatoris sp. nov., from American alligators. Int J Syst Evol Microbiol 51:419–424PubMedCrossRefGoogle Scholar
  23. Brown DR, Talkington DF, Thacker WL, Brown MB, Dillehay DL, Tully JG (2001b) Mycoplasma microti sp. nov., isolated from the respiratory tract of prairie voles (Microtus ochrogaster). Int J Syst Evol Microbiol 51:409–412PubMedCrossRefGoogle Scholar
  24. Brown DR, Klein PA, McLaughlin GS, Schumacher IM, Jacobson ER, Adams HP, Tully JG (2001c) Mycoplasma agassizii sp. nov., isolated from the upper respiratory tract of the desert tortoise (Gopherus agassizii) and the gopher tortoise (Gopherus polyphemus). Int J Syst Evol Microbiol 51:413–418PubMedCrossRefGoogle Scholar
  25. Brown DR, Merritt JL, Jacobson ER, Klein PA, Tully JG, Brown MB (2004) Mycoplasma testudineum sp. nov., from a desert tortoise (Gopherus agassizii) with upper respiratory tract disease. Int J Syst Evol Microbiol 54:1527–1529PubMedCrossRefGoogle Scholar
  26. Brown DR, Demcovitz DL, Plourdé DR, Potter SM, Hunt ME, Jones RD, Rotstein DS (2006) Mycoplasma iguanae sp. nov., from a green iguana (Iguana iguana) with vertebral disease. Int J Syst Evol Microbiol 56:761–764PubMedCrossRefGoogle Scholar
  27. Brown DR, Bradbury JM, Johansson K-E (2010a) Family I. Acholeplasmataceae Edward and Freundt 1970, 1AL. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology.The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol 4. Springer, New York, pp 687–696Google Scholar
  28. Brown DR, Bradbury JM, Whitcomb RF (2010b) Family I. Entoplasmataceae Tully, Bové, Laigart and Whitcomb 1993, 380VP. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol 4. Springer, New York, pp 645–653Google Scholar
  29. Brown DR, May M, Bradbury JM, Balish MF, Calcutt MJ, Glass JI, Tasker S, Messick JB, Johansson K-E, Newmark H (2010c) Genus I. Mycoplasma Nowak 1929, 1349 nom. cons. Jud. Comm. Opin. 22, 1958, 166AL. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol 4. Springer, New York, pp 575–613Google Scholar
  30. Brown DR, May M, Bradbury JM, Johansson K-E (2010d). Class I. Mollicutes Edward and Freundt 1967, 267AL. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol. 4. Springer, New York, pp 568–573Google Scholar
  31. Brown DR, May M, Bradbury JM, Johansson K-E, Newmark H (2010e). Family I. Mycoplasmataceae Freundt 1955, 71AL emend. Tully, Bové, Laigart and Whitcomb 1993, 382. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol 4. Springer, New York, pp 575–639Google Scholar
  32. Campbell C, Adeolu M, Gupta RS (2015) Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov. Int J Syst Evol Microbiol 65:3203–3215PubMedCrossRefGoogle Scholar
  33. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973PubMedPubMedCentralCrossRefGoogle Scholar
  34. Carmichael LE, St George TD, Sullivan ND, Horsfall N (1972) Isolation, propagation, and characterization studies of an ovine Mycoplasma responsible for proliferative interstitial pneumonia. Cornell Vet 62:654–679PubMedGoogle Scholar
  35. Chandra G, Chater KF (2014) Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences. FEMS Microbiol Rev 38:345–379PubMedCrossRefGoogle Scholar
  36. Clark R (1942) Eperythrozoon felis (sp. nov.) in a cat. J Afr Vet Med Assoc 13:15–16Google Scholar
  37. Cole BC, Golightly L, Ward JR (1967) Characterization of mycoplasma strains from cats. J Bacteriol 94:1451–1458PubMedPubMedCentralGoogle Scholar
  38. DaMassa AJ, Tully JG, Rose DL, Pitcher D, Leach RH, Cottew GS (1994) Mycoplasma auris sp. nov., Mycoplasma cottewii sp. nov., and Mycoplasma yeatsii sp. nov., new sterol-requiring mollicutes from the external ear canals of goats. Int J Syst Bacteriol 44:479–484PubMedCrossRefGoogle Scholar
  39. Del Giudice RA, Carski TR, Barile MF, Lemcke RM, Tully JG (1971) Proposal for classifying human strain navel and related simian mycoplasmas as Mycoplasma primatum sp. n. J Bacteriol 108:439–445Google Scholar
  40. Del Giudice RA, Purcell RH, Carski TR, Chanock RM (1974) Mycoplasma lipophilum sp. nov. Int J Syst Bacteriol 24:147–153CrossRefGoogle Scholar
  41. Del Giudice RA, Tully JG, Rose DL, Cole RM (1985) Mycoplasma pirum sp. nov., a terminal structured mollicute from cell cultures. Int J Syst Bacteriol 35:285–291CrossRefGoogle Scholar
  42. Del Giudice RA, Rose DL, Tully JG (1995) Mycoplasma adleri sp. nov., an isolate from a goat. Int J Syst Bacteriol 45:29–31PubMedCrossRefGoogle Scholar
  43. Dutilh BE, Snel B, Ettema TJ, Huynen MA (2008) Signature genes as a phylogenomic tool. Mol Biol Evol 25:1659–1667PubMedPubMedCentralCrossRefGoogle Scholar
  44. Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195PubMedPubMedCentralCrossRefGoogle Scholar
  45. Edward DF (1955) A suggested classification and nomenclature for organisms of the pleuropneumonia group. Int Bull Bacteriol Nomencl Taxon 5:85–93Google Scholar
  46. Edward DF, Kanarek AD (1960) Organisms of the pleuropneumonia group of avian origin: their classification into species. Ann New York Acad Sci 79:696–702CrossRefGoogle Scholar
  47. Edward DG, Freundt EA (1967) Proposal for Mollicutes as name of the class established for the order Mycoplasmatales. Int J Syst Bacteriol 17:267–268CrossRefGoogle Scholar
  48. Erickson BZ, Ross RF, Rose DL, Tully JG, Bové JM (1986) Mycoplasma hyopharyngis, a new species from swine. Int J Syst Bacteriol 36:55–59CrossRefGoogle Scholar
  49. Fadiel A, Eichenbaum KD, El Semary N, Epperson B (2007) Mycoplasma genomics: tailoring the genome for minimal life requirements through reductive evolution. Front Biosci 12:2020–2028PubMedCrossRefGoogle Scholar
  50. Fettweis JM, Serrano MG, Huang B, Brooks P, Glascock AL, Sheth NU, Vaginal Microbiome Consortium, Strauss JF III, Jefferson KK, Buck GA (2014) An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease. PLoS ONE 9:e110943PubMedPubMedCentralCrossRefGoogle Scholar
  51. Firraro G, Brown DR (2011) 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 Microbiol 61:695–697CrossRefGoogle Scholar
  52. Foley JE, Pedersen NC (2001) ‘Candidatus Mycoplasma haemominutum’, a low-virulence epierythrocytic parasite of cats. Int J Syst Evol Microbiol 51:815–817PubMedCrossRefGoogle Scholar
  53. Forrest M, Bradbury JM (1984a) Mycoplasma glycophilum, a new species of avian origin. J Gen Microbiol 130:597–603PubMedGoogle Scholar
  54. Forrest M, Bradbury JM (1984b) Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 15. Int J Syst Bacteriol 34:355–357CrossRefGoogle Scholar
  55. Forsyth MH, Tully JG, Gorton TS, Hinckley L, Frasca S Jr, Van Kruiningen HJ, Geary SJ (1996) Mycoplasma sturni sp. nov., from the conjunctiva of a European starling (Sturnus vulgaris). Int J Syst Bacteriol 46:716–719PubMedCrossRefGoogle Scholar
  56. Freundt EA (1953) The occurrence of Micromyces (pleuropneumonia-like organisms) in the female genito-urinary tract. Acta Pathol Microbiol Scand 32:48–480Google Scholar
  57. Freundt EA (1955) The classification of the pleuropneumonia group of organisms (Borrelomycetales). Int Bull Bacteriol Nomencl Taxon 5:67–78Google Scholar
  58. Freundt EA, Taylor-Robinson D, Purcell RH, Chanock RM, Black FT (1974) Proposal of Mycoplasma buccale nom. nov. and Mycoplasma faucium nom. nov. for Mycoplasma orale “types” 2 and 3, respectively. Int J Syst Bacteriol 24:252–255CrossRefGoogle Scholar
  59. Gao B, Gupta RS (2005) Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 55:2401–2412PubMedCrossRefGoogle Scholar
  60. Gao B, Gupta RS (2012) Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 76:66–112PubMedPubMedCentralCrossRefGoogle Scholar
  61. Gasparich GE (2014) The family Entomoplasmataceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Firmicutes and Tenericutes. Springer, Berlin, pp 505–514Google Scholar
  62. Giebel J, Meier J, Binder A, Flossdorf J, Poveda JB, Schmidt R, Kirchhoff H (1991) Mycoplasma phocarhinis sp. nov. and Mycoplasma phocacerebrale sp. nov., two new species from harbor seals (Phoca vitulina L.). Int J Syst Bacteriol 41:39–44PubMedCrossRefGoogle Scholar
  63. Gourlay RN, Leach RH (1970) A new Mycoplasma species isolated from pneumonic lungs of calves (Mycoplasma dispar sp. nov.). J Med Microbiol 3:111–123PubMedCrossRefGoogle Scholar
  64. Gourlay RN, Leach RH, Howard CJ (1974) Mycoplasma verecundum, a new species isolated from bovine eyes. J Gen Microbiol 81:475–484PubMedCrossRefGoogle Scholar
  65. Gourlay RN, Wyld SG, Leach RH (1977) Mycoplasma alvi, a new species from bovine intestinal and urogenital tracts. Int J Syst Bacteriol 27:86–96CrossRefGoogle Scholar
  66. Gourlay RN, Wyld SG, Leach RH (1978) Mycoplasma sualvi, a new species from the intestinal and urogenital tracts of pigs. Int J Syst Bacteriol 28:289–292CrossRefGoogle Scholar
  67. Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A (2014) Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet 10:1004363CrossRefGoogle Scholar
  68. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321PubMedCrossRefGoogle Scholar
  69. Gundersen DE, Lee IM, Rehner SA, Davis RE, Kingsbury DT (1994) Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classification. J Bacteriol 176:5244–5254PubMedPubMedCentralCrossRefGoogle Scholar
  70. Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62:1435–1491PubMedPubMedCentralGoogle Scholar
  71. Gupta RS (2000) The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24:367–402PubMedCrossRefGoogle Scholar
  72. Gupta RS (2014) Identification of conserved indels that are useful for classification and evolutionary studies. In: Goodfellow M, Sutcliffe I, Chun J (eds) Methods in microbiology. New approaches to prokaryotic systematics. Academic Press, Cambridge, pp 153–182CrossRefGoogle Scholar
  73. Gupta RS (2016) Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin’s views on classification. FEMS Microbiol Rev 40:520–553PubMedCrossRefGoogle Scholar
  74. Gupta RS, Naushad S, Baker S (2015) 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 Microbiol 65:1050–1069PubMedCrossRefGoogle Scholar
  75. Gupta RS, Naushad S, Fabros R, Adeolu M (2016) A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov. Antonie van Leeuwenhoek 109:565–587PubMedCrossRefGoogle Scholar
  76. Gupta RS, Nanda A, Khadka B (2017) Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales. PLoS ONE 12:e0172176PubMedPubMedCentralCrossRefGoogle Scholar
  77. Gupta RS, Lo B, Son J (2018) Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera. Front Microbiol 9, 67Google Scholar
  78. Hale HH, Helmboldt CF, Plastridge WN, Stula EF (1962) Bovine mastitis caused by a Mycoplasma species. Cornell Vet. 52:582–591PubMedGoogle Scholar
  79. Hassan FMN, Gupta RS (2018) Novel sequence features of DNA repair genes/proteins from Deinococcus species implicated in protection from oxidatively generated damage. Genes 9:149CrossRefGoogle Scholar
  80. Heltander Königsson M, Pettersson B, Johansson K-E (2001) Phylogeny of the seal mycoplasmas Mycoplasma phocae corrig., Mycoplasma phocicerebrale corrig. and Mycoplasma phocirhinis corrig. based on sequence analysis of 16S rDNA. Int J Syst Evol Microbiol 51:1389–1393PubMedCrossRefGoogle Scholar
  81. Hill AC (1971) Mycoplasma caviae, a new species. J Gen Microbiol 65:109–113PubMedCrossRefGoogle Scholar
  82. Hill AC (1983a) Mycoplasma collis, a new species isolated from rats and mice. Int J Syst Bacteriol 33:847–851CrossRefGoogle Scholar
  83. Hill AC (1983b) Mycoplasma cricetuli, a new species from the conjunctivas of Chinese hamsters. Int J Syst Bacteriol 33:113–117CrossRefGoogle Scholar
  84. Hill AC (1984) Mycoplasma cavipharyngis, a new species isolated from the nasopharynx of guinea-pigs. J Gen Microbiol 130:3183–3188PubMedGoogle Scholar
  85. Hill AC (1985) Mycoplasma testudinis, a new species isolated from a tortoise. Int J Syst Bacteriol 35:489–492CrossRefGoogle Scholar
  86. Hill AC (1986) Mycoplasma felifaucium, a new species isolated from the respiratory tract of pumas. J Gen Microbiol 132:1923–1928PubMedGoogle Scholar
  87. Hill AC (1988) Validation of the publication of new names and new combinations previously effectively published outside the IJSB: List No. 27. Int J Syst Bacteriol 38:449CrossRefGoogle Scholar
  88. Hill AC (1989) Validation of the publication of new names and new combinations previously effectively published outside the IJSB (List No. 30). Int J Syst Bacteriol 39:371CrossRefGoogle Scholar
  89. Hill AC (1991a) Mycoplasma oxoniensis, a new species isolated from Chinese hamster conjunctivas. Int J Syst Bacteriol 41:21–25PubMedCrossRefGoogle Scholar
  90. Hill AC (1991b) Mycoplasma spermatophilum, a new species isolated from human spermatozoa and cervix. Int J Syst Bacteriol 41:229–233PubMedCrossRefGoogle Scholar
  91. Hill AC (1992) Mycoplasma simbae sp. nov., Mycoplasma leopharyngis sp. nov., and Mycoplasma leocaptivus sp. nov., isolated from lions. Int J Syst Bacteriol 42:518–523PubMedCrossRefGoogle Scholar
  92. Hill AC (1993) Mycoplasma indiense sp. nov., isolated from the throats of nonhuman primates. Int J Syst Bacteriol 43:36–40PubMedCrossRefGoogle Scholar
  93. Hugenholtz P, Skarshewski A, Parks DH (2016) Genome-based microbial taxonomy coming of age. Cold Spring Harbor Perspect Biol. 8:1–11CrossRefGoogle Scholar
  94. Jasper DE, Ernø H, Dellinger JD, Christiansen C (1981) Mycoplasma californicum, a new species from cows. Int J Syst Bacteriol 31:339–345CrossRefGoogle Scholar
  95. Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998) Multiple sequence alignment with Clustal X. Trends Biochem Sci 23:403–405PubMedCrossRefGoogle Scholar
  96. Johansson K-E, Pettersson B (2002) Taxonomy of Mollicutes. In: Razin S, Herrmann R (eds) Molecular biology and pathogenicity of mycoplasmas. Springer, Boston, pp 1–29Google Scholar
  97. Jordan FTW, Ernø H, Cottew GS, Hinz KH, Stipkovits L (1982) Characterization and taxonomic description of five mycoplasma serovars (serotypes) of avian origin and their elevation to species rank and further evaluation of the taxonomic status of Mycoplasma synoviae. Int J Syst Bacteriol 32:108–115CrossRefGoogle Scholar
  98. Jores J, Fischer A, Sirand-Pugnet P, Thomann A, Liebler-Tenorio EM, Schnee C, Santana-Cruz I, Heller M, Frey J (2015) Mycoplasma feriruminatoris sp. nov., a fast-growing Mycoplasma species isolated from wild Caprinae. Syst Appl Microbiol 36:533–538CrossRefGoogle Scholar
  99. Khadka B, Gupta RS (2017) Identification of a conserved 8 aa insert in the PIP5 K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role. Proteins 85:1454–1467PubMedCrossRefGoogle Scholar
  100. Kikuth W (1928) Über einen neuen Anämieerreger; Bartonella canis nov. spec. Klin Wochenschr 7:1729–1730CrossRefGoogle Scholar
  101. Kim KS, Ko KS, Chang M-W, Hahn TW, Hong SK, Kook YH (2003) Use of rpoB sequences for phylogenetic study of Mycoplasma species. FEMS Microbiol Lett 226:299–305PubMedCrossRefGoogle Scholar
  102. Kirchhoff H (1978) Mycoplasma equigenitalium, a new species from the cervix region of mares. Int J Syst Bacteriol 28:496–502CrossRefGoogle Scholar
  103. Kirchhoff H, Beyene P, Fischer M, Flossdorf J, Heitmann J, Khattab B, Lopatta D, Rosengarten R, Seidel G, Yousef C (1987) Mycoplasma mobile sp. nov., a new species from fish. Int J Syst Bacteriol 37:192–197CrossRefGoogle Scholar
  104. Kirchhoff H, Schmidt R, Lehmann H, Clark HW, Hill AC (1996) Mycoplasma elephantis sp. nov., a new species from elephants. Int J Syst Bacteriol 46:437–441CrossRefGoogle Scholar
  105. Kirchhoff H, Mohan K, Schmidt R, Runge MR, Brown DR, Brown MB, Foggin CM, Muvavarirwa P, Lehmann H, Flossdorf J (1997) Mycoplasma crocodyli sp. nov., a new species from crocodiles. Int J Syst Bacteriol 47:742–746PubMedCrossRefGoogle Scholar
  106. Kobayashi H, Runge M, Schmidt R, Kubo M, Yamamoto K, Kirchhoff H (1997) Mycoplasma lagogenitalium sp. nov., from the preputial smegma of Afghan pikas (Ochotona rufescens rufescens). Int J Syst Bacteriol 47:1208–1211PubMedCrossRefGoogle Scholar
  107. Kong F, Gilbert GL (2004) Postgenomic taxonomy of human ureaplasmas - a case study based on multiple gene sequences. Int J Syst Evol Microbiol 54:1815–1821PubMedCrossRefGoogle Scholar
  108. Krasteva I, Inglis NF, Sacchini F, Nicholas R, Ayling R, Churchward CP, March J, Lainson A, Mclean K, Hughes V, Imrie L, Manson E, Clark J, Pini A, Smith DGE (2014) Proteomic characterisation of two strains of Mycoplasma mycoides subsp. mycoides of differing pathogenicity. J Proteomics Bioinform 13:2Google Scholar
  109. Kreier JP, Tistic M (1963) Anaplasmosis. XII. The growth and survival in deer and sheep of the parasites present in the blood of calves infected with the Oregon strain of Anaplasma marginale. Am J Vet Res 24:697–702PubMedGoogle Scholar
  110. Langford EV, Leach RH (1973) Characterization of a mycoplasma isolated from infectious bovine keratoconjunctivitis: M. bovoculi sp. nov. Can J Microbiol 19:1435–1444PubMedCrossRefGoogle Scholar
  111. Langford EV, Ruhnke HL, Onoviran O (1976) Mycoplasma canadense, a new bovine species. Int J Syst Bacteriol 26:212–219CrossRefGoogle Scholar
  112. Lawson PA, Citron DM, Tyrrell KL, Finegold SM (2016) Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O’Toole 1935) Prevot 1938. Anaerobe 40:95–99PubMedCrossRefGoogle Scholar
  113. Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25:1307–1320PubMedCrossRefGoogle Scholar
  114. Leach RH (1967) Comparative studies of mycoplasma of bovine orign. Ann New York Acad Sci 143:305–316CrossRefGoogle Scholar
  115. Leach RH (1973) Further studies on classification of bovine strains of Mycoplasmatales, with proposals for new species, Acholeplasma modicum and Mycoplasma alkalescens. J Gen Microbiol 75:135–153PubMedCrossRefGoogle Scholar
  116. Leclercq S, Dittmer J, Bouchon D, Cordaux R (2014) Phylogenomics of “Candidatus Hepatoplasma crinochetorum,” a lineage of mollicutes associated with noninsect arthropods. Genome Biol Evol 6:407–415PubMedPubMedCentralCrossRefGoogle Scholar
  117. Lemcke RM, Kirchhoff H (1979) Mycoplasma subdolum, a new species isolated from horses. Int J Syst Bacteriol 29:42–50CrossRefGoogle Scholar
  118. Lemcke RM, Poland J (1980) Mycoplasma fastidiosum: a new species from horses. Int J Syst Bacteriol 30:151–162CrossRefGoogle Scholar
  119. Lo SC, Hayes MM, Tully JG, Wang RY-H, Kotani H, Pierce PF, Rose DL, Shih JW-K (1992) Mycoplasma penetrans sp. nov., from the urogenital tract of patients with AIDS. Int J Syst Bacteriol 42:357–364PubMedCrossRefGoogle Scholar
  120. Madden DL, Moats KE, London WT, Matthew EB, Sever JL (1974) Mycoplasma moatsii, a new species isolated from recently imported Grivit monkeys (Cercopithecus aethiops). Int J Syst Bacteriol 24:459–464CrossRefGoogle Scholar
  121. Maniloff J (2002) Phylogeny and evolution. In: Razin S, Herrmann R (eds) Molecular biology and pathogenicity of mycoplasmas. Springer, Boston, pp 31–43CrossRefGoogle Scholar
  122. Manso-Silván L, Perrier X, Thiaucourt F (2007) Phylogeny of the Mycoplasma mycoides cluster based on analysis of five conserved protein-coding sequences and possible implications for the taxonomy of the group. Int J Syst Evol Microbiol 57:2247–2258PubMedCrossRefGoogle Scholar
  123. Manso-Silván L, Vilei EM, Sachse K, Djordjevic SP, Thiaucourt F, Frey J (2009) Mycoplasma leachii sp. nov. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and reclassification of Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides subsp. capri. Int J Syst Evol Microbiol 59:1353–1358PubMedCrossRefGoogle Scholar
  124. Maré CJ, Switzer WP (1965) New species: Mycoplasma hypopneumoniae; a causative agent of virus pig pneumonia. Vet Med Small Animal Clin 60:841–846Google Scholar
  125. Martini M, Marcone C, Lee I-M, Firrao G (2014) The family Acholeplasmataceae (including Phytoplasmas). In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Firmicutes and Tenericutes. Springer, Berlin, pp 469–504Google Scholar
  126. May M, Brown DR (2014) International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of Mollicutes. Minutes of the meetings (closed and open), 1 and 5 June 2014, Blumenau SC, Brazil. Int J Syst Evol Microbiol 64:3904–3906PubMedCrossRefGoogle Scholar
  127. May M, Balish MF, Blanchard A (2014) In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Firmicutes and Tenericutes. Springer, Berlin, pp 515–550Google Scholar
  128. Mayer M (1921) Über einige bakterienähnliche Parasiten der Erythrozyten bei Menschen und Tieren. Arch Schiffs Tropenhyg 25:150–152Google Scholar
  129. McGarrity GJ, Rose DL, Kwiatkowski V, Dion AS, Phillips DM, Tully JG (1983) Mycoplasma muris, a new species from laboratory mice. Int J Syst Bacteriol 33:350–355CrossRefGoogle Scholar
  130. Messick JB, Walker PG, Raphael W, Berent L, Shi X (2002) ‘Candidatus Mycoplasma haemodidelphidis’ sp. nov., ‘Candidatus Mycoplasma haemolamae’ sp. nov. and Mycoplasma haemocanis comb. nov., haemotrophic parasites from a naturally infected opossum (Didelphis virginiana), alpaca (Lama pacos) and dog (Canis familiaris): phylogenetic and secondary structural relatedness of their 16S rRNA genes to other mycoplasmas. Int J Syst Evol Microbiol 52:693–698PubMedGoogle Scholar
  131. Meyling A, Friis NF (1972) Serological identification of a new porcine mycoplasma species, Mycoplasma flocculare. Acta Vet Scand 13:287–289PubMedGoogle Scholar
  132. Möller Palau-Ribes F, Enderlein D, Hagen N, Herbst W, Hafez HM, Lierz M (2016) Description and prevalence of Mycoplasma ciconiae sp. nov. isolated from white stork nestlings (Ciconia ciconia). Int J Syst Evol Microbiol 66:3477–3484PubMedCrossRefGoogle Scholar
  133. Murray RGE (1984) The higher taxa, or, a place for everything? In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 1. Williams & Wilkins, Baltimore, pp 31–34Google Scholar
  134. Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93:10268–10273PubMedPubMedCentralCrossRefGoogle Scholar
  135. Naushad HS, Lee B, Gupta RS (2014) Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. Int J Syst Evol Microbiol 64:366–383PubMedCrossRefGoogle Scholar
  136. Neimark H, Johansson K-E, Rikihisa Y, Tully JG (2001) Proposal to transfer some members of the genera Haemobartonella and Eperythrozoon to the genus Mycoplasma with descriptions of ‘Candidatus Mycoplasma haemofelis’, ‘Candidatus Mycoplasma haemomuris’, ‘Candidatus Mycoplasma haemosuis’ and ‘Candidatus Mycoplasma wenyonii’. Int J Syst Evol Microbiol 51:891–899PubMedCrossRefGoogle Scholar
  137. Neimark H, Johansson K-E, Rikihisa Y, Tully JG (2002) Revision of haemotrophic Mycoplasma species names. Int J Syst Evol Microbiol 52:683PubMedCrossRefGoogle Scholar
  138. Neimark H, Hoff B, Ganter M (2004) Mycoplasma ovis comb. nov. (formerly Eperythrozoon ovis), an epierythrocytic agent of haemolytic anaemia in sheep and goats. Int J Syst Evol Micorbiol 54:365–371CrossRefGoogle Scholar
  139. Neimark H, Peters W, Robinson BL, Stewart LB (2005) Phylogenetic analysis and description of Eperythrozoon coccoides, proposal to transfer to the genus Mycoplasma as Mycoplasma coccoides comb. nov. and Request for an Opinion. Int J Syst Evol Microbiol 55:1385–1391PubMedCrossRefGoogle Scholar
  140. Neitz WO, Alexander RA, du Toit OJ (1934) Eperythrozoon ovis (sp. nov.) infection in sheep. Onderstepoort J Vet Sci 3:263–274Google Scholar
  141. Nowak J (1929) Morphologie, nature et cycle évolutif du microbe de la péripneumonie des bovidés. Ann Inst Pasteur 43:1330–1352Google Scholar
  142. Olson NO, Kerr KM, Campbell A (1964) Control of infectious synovitis 13. The antigen study of three strains. Avian Dis 8:209–214CrossRefGoogle Scholar
  143. Oshima K, Nishida H (2007) Phylogenetic relationships among mycoplasmas based on the whole genomic information. J Mol Evol 65:249–258PubMedCrossRefGoogle Scholar
  144. Panangala VS, Stringfellow JS, Dybvig K, Woodard A, Sun F, Rose DL, Gresham MM (1993) Mycoplasma corogypsi sp. nov., a new species from the footpad abscess of a black vulture. Coragyps atratus. Int J Syst Bacteriol 43:585–590PubMedCrossRefGoogle Scholar
  145. Parker CT, Tindall BJ, Garrity GM (2016) International code of nomenclature of Prokaryotes. Prokaryotic code 2008 revision). Int J Syst Evol Microbiol. Google Scholar
  146. Parte AC (2014) LPSN-list of prokaryotic names with standing in nomenclature. Nucl Acids Res 42:D613–D616PubMedCrossRefGoogle Scholar
  147. Peters IR, Helps CR, McAuliffe L, Neimark H, Lappin MR, Gruffydd-Jones TJ, Day MJ, Hoelzle LE, Willi B, Meli M, Hofmann-Lehmann R, Tasker S (2008) RNase P RNA gene (rnpB) phylogeny of hemoplasmas and other Mycoplasma species. J Clin Microbiol 46:1873–1877PubMedPubMedCentralCrossRefGoogle Scholar
  148. Pettersson B, Tully JG, Bolske G, Johansson KE et al (2000) EUpdated phylogenetic description of the Mycoplasma hominis cluster (Weisburg et al. 1989) based on 16S rDNA sequences. Int J Syst Evol Microbiol 50:291–301PubMedCrossRefGoogle Scholar
  149. Pitcher DG, Windsor D, Windsor H, Bradbury JM, Yavari C, Jensen JS, Ling C, Webster D (2005) Mycoplasma amphoriforme sp. nov., isolated from a patient with chronic bronchopneumonia. Int J Syst Evol Microbiol 55:2589–2594PubMedCrossRefGoogle Scholar
  150. Pollack JD, Williams MV, Banzon J, Jones MA, Harvey L, Tully JG (1996) Comparative metabolism of Mesoplasma, Entomoplasma, Mycoplasma, and Acholeplasma. Int J Syst Bacteriol 46:885–890PubMedCrossRefGoogle Scholar
  151. Poveda JB, Giebel J, Flossdorf J, Meier J, Kirchhoff H (1994) Mycoplasma buteonis sp. nov., Mycoplasma falconis sp. nov., and Mycoplasma gypis sp. nov., three species from birds of prey. Int J Syst Bacteriol 44:94–98CrossRefGoogle Scholar
  152. Price MN, Dehal PS, Arkin AP (2010) FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490PubMedPubMedCentralCrossRefGoogle Scholar
  153. Razin S (1992) Mycoplasma taxonomy and ecology. In: Maniloff J, McElhaney RN, Finch LR, Baseman JB (eds) Mycoplasmas: molecular biology and pathogenesis. American Society for Microbiology, Washington, D.C., pp 3–22Google Scholar
  154. Razin S, Herrmann R (2002) Molecular biology and pathogenicity of mycoplasmas. Kluwer Academic/Plenum Publishers, New YorkCrossRefGoogle Scholar
  155. Razin S, Yogev D, Naot Y (1998) Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62:1094–1156PubMedPubMedCentralGoogle Scholar
  156. Regassa LB (2014) The Family Spiroplasmataceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Firmicutes and Tenericutes. Springer, Berlin, pp 551–567Google Scholar
  157. Roberts DH (1964) The isolation of an influenza A virus and a mycoplasma associated with duck sinusitis. Vet Rec 76:470–473Google Scholar
  158. Rokas A, Holland PW (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15:454–459PubMedCrossRefGoogle Scholar
  159. Rose DL, Tully JG, Langford EV (1978) Mycoplasma citelli, a new species from ground squirrels. Int J Syst Bacteriol 28:567–572CrossRefGoogle Scholar
  160. Rosendal S (1973) Mycoplasma cynos, a new canine Mycoplasma species. Int J Syst Bacteriol 23:49–54CrossRefGoogle Scholar
  161. Rosendal S (1974) Mycoplasma molare, a new canine Mycoplasma species. Int J Syst Bacteriol 24:125–130CrossRefGoogle Scholar
  162. Rosendal S (1975) Canine mycoplasmas: serological studies of type and reference strains, with a proposal for the new species, Mycoplasma opalescens. APMIS 83:463–470Google Scholar
  163. Ross RF, Karmon JA (1970) Heterogeneity among strains of Mycoplasma granularum and identification of Mycoplasma hyosynoviae, sp. n. J Bacteriol 103:707–713PubMedPubMedCentralGoogle Scholar
  164. Ruhnke HL, Madoff S (1992) Mycoplasma phocidae sp. nov., isolated from harbor seals (Phoca vitulina L.). Int J Syst Bacteriol 42:211–214PubMedCrossRefGoogle Scholar
  165. Sabin AB (1941) The filtrable microorganisms of the pleuropneumonia group. Bacteriol Rev 5:331–335PubMedPubMedCentralGoogle Scholar
  166. Salih MM, Friis NF, Arseculeratne SN, Freundt EA, Christiansen C (1983) Mycoplasma mustelae, a new species from mink. Int J Syst Bacteriol 33:476–479CrossRefGoogle Scholar
  167. Schilling V (1928) Eperythrozoon coccoides, eine neue durch Splenektomie aktivierbare Dauerinfektion der weissen Maus. Klin Wschr 7:1853–1855CrossRefGoogle Scholar
  168. Schoeffler AJ, May AP, Berger JM (2010) A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucl Acids Res 38:7830–7844PubMedPubMedCentralCrossRefGoogle Scholar
  169. Sha BE, Zariffard MR, Wang QJ, Chen HY, Bremer J, Cohen MH, Spear GT (2005) Female genital-tract HIV load correlates inversely with Lactobacillus species but positively with bacterial vaginosis and Mycoplasma hominis. J Infect Dis 191:25–32PubMedCrossRefGoogle Scholar
  170. Shepard MC, Lunceford CD, Ford DK, Purcell RH, Taylor-Robinson D, Razin S, Black FT (1974) Ureaplasma urealyticum gen. nov., sp. nov.: proposed nomenclature for the human T (T-strain) mycoplasmas. Int J Syst Bacteriol 24:160–171CrossRefGoogle Scholar
  171. Shimizu T, Ernø H, Nagatomo H (1978) Isolation and characterization of Mycoplasma columbinum and Mycoplasma columborale, two new species from pigeons. Int J Syst Bacteriol 28:538–546CrossRefGoogle Scholar
  172. Singh B, Gupta RS (2009) Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics 281:361–373PubMedCrossRefGoogle Scholar
  173. Sirand-Pugnet P, Citti C, Barré A, Blanchard A (2007) Evolution of mollicutes: down a bumpy road with twists and turns. Res Microbiol 158:754–766PubMedCrossRefGoogle Scholar
  174. Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420CrossRefGoogle Scholar
  175. Somerson NL, Taylor-Robinson D, Chanock RM (1963) Hemolysin production as an aid in the identification and quantitation of Eaton agent (Mycoplasma pneumoniae). Am J Hyg 77:122–128PubMedGoogle Scholar
  176. Spergser J, Langer S, Muck S, Macher K, Szostak M, Rosengarten R, Busse HJ (2011) Mycoplasma mucosicanis sp. nov., isolated from the mucosa of dogs. Int J Syst Evol Microbiol 61:716–721PubMedCrossRefGoogle Scholar
  177. Splitter EJ (1950) Eperythrozoon suis n. sp. and Eperythrozoon parvum n. sp., two new blood parasites of swine. Science 111:513–514PubMedCrossRefGoogle Scholar
  178. Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313PubMedPubMedCentralCrossRefGoogle Scholar
  179. Suárez-Pérez A, Ramírez AS, Rosales RS, Calabuig P, Poveda C, Rosselló-Móra R, Nicholas RA, Poveda JB (2012) Mycoplasma neophronis sp. nov., isolated from the upper respiratory tract of Canarian Egyptian vultures (Neophron percnopterus majorensis). Int J Syst Evol Microbiol 62:1321–1325PubMedCrossRefGoogle Scholar
  180. Switzer WP (1955) Studies on infectious atrophic rhinitis. IV. Characterization of a pleuropneumonia-like organism isolated from the nasal cavities of swine. Am J Vet Res 16:540–544PubMedGoogle Scholar
  181. Tagawa M, Matsumoto K, Inokuma H (2008) Molecular detection of Mycoplasma wenyonii and ‘Candidatus Mycoplasma haemobos’ in cattle in Hokkaido, Japan. Vet Microbiol 132:177–180PubMedCrossRefGoogle Scholar
  182. Taylor-Robinson D, Canchola J, Fox H, Chanock RM (1964) A newly identified oral mycoplasma (M. orale) and its relationship to other human mycoplasmas. Am J Hyg 80:135–148PubMedGoogle Scholar
  183. Thompson CC, Vieira NM, Vicente AC, Thompson FL (2011) Towards a genome based taxonomy of Mycoplasmas. Infect Genet Evol 11:1798–1804PubMedCrossRefGoogle Scholar
  184. Tindall BJ (1999) Misunderstanding the bacteriological code. Int J Syst Bacteriol 49:1313–1316PubMedCrossRefGoogle Scholar
  185. Tindall BJ (2014) The Request for an Opinion that the current use of the genus name Mycoplasma be maintained and Mycoplasma coccoides be considered a legitimate name is denied. Opinion 92. Int J Syst Evol Microbiol 64:3586–3587PubMedCrossRefGoogle Scholar
  186. Toth KF, Harrison N, Sears BB (1994) Phylogenetic relationships among members of the class Mollicutes deduced from rps3 gene sequences. Int J Syst Bacteriol 44:119–124PubMedCrossRefGoogle Scholar
  187. Trüper HG, de’Clari L (1998) Taxonomic note: erratum and correction of further specific epithets formed as substantives (nouns) ‘in apposition’. Int J Syst Bacteriol 48:615CrossRefGoogle Scholar
  188. Tully JG, Barile MF, Del Giudice RA, Carski TR, Armstrong D, Razin S (1970) Proposal for classifying strain PG-24 and related canine mycoplasmas as Mycoplasma edwardii sp. n. J Bacteriol 101:346–349PubMedPubMedCentralGoogle Scholar
  189. Tully JG, Barile MF, Edward DG, Theodore TS, Ernø H (1974) Characterization of some caprine mycoplasmas, with proposals for new species, Mycoplasma capricolum and Mycoplasma putrefaciens. J Gen Microbiol 85:102–120PubMedCrossRefGoogle Scholar
  190. Tully JG, Taylor-Robinson DAVI, Rose DL, Cole RM, Bove JM (1983) Mycoplasma genitalium, a new species from the human urogenital tract. Int J Syst Bacteriol 33:387–396CrossRefGoogle Scholar
  191. Tully JG, Bové JM, Laigret F, Whitcomb RF (1993) Revised taxonomy of the class Mollicutes: proposed elevation of a monophyletic cluster of arthropod-associated mollicutes to ordinal rank (Entomplasmatales ord. nov.), with provision for familiar 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 Bacteriol 43:378–385CrossRefGoogle Scholar
  192. Tyzzer EE, Weiman D (1939) Haemobartonella n.g. (Bartonella olim pro parte), H. microti n. sp. of the field vole. Microtus pennsylvanicus. Am J Hyg 40:157–241Google Scholar
  193. Uilenberg G, Thiaucourt F, Jongejan F (2004) On molecular taxonomy: what is in a name? Exp Appl Aracol 32:301–312CrossRefGoogle Scholar
  194. Uilenberg G, Thiaucourt F, Jongejan F (2006) Mycoplasma and Eperythrozoon (Mycoplasmataceae). Comments on a recent paper. Int J Syst Evol Microbiol 56:13–14PubMedCrossRefGoogle Scholar
  195. Volokhov DV, Neverov AA, George J, Kong H, Liu SX, Anderson C, Davidson MK, Chizhikov V (2007) Genetic analysis of housekeeping genes of members of the genus Acholeplasma: phylogeny and complementary molecular markers to the 16S rRNA gene. Mol Phylogenet Evol 44:699–710PubMedCrossRefGoogle Scholar
  196. Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE (2012) RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae. Mol Phylogenet Evol 62:515–528PubMedCrossRefGoogle Scholar
  197. Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, WoykeT Klotz MG, Hugenholtz P (2017) Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 8:682PubMedPubMedCentralCrossRefGoogle Scholar
  198. Waites KB, Talkington DF (2004) Mycoplasma pneumoniae and its role as a human pathogen. Clin Microbiol Rev 17:697–728PubMedPubMedCentralCrossRefGoogle Scholar
  199. Wang Z, Wu M (2013) A phylum-level bacterial phylogenetic marker database. Mol Biol Evol 30:1258–1262PubMedCrossRefGoogle Scholar
  200. Weisburg WG, Tully JG, Rose DL, Petzel JP, Oyaizu H, Yang D, Mandelco L, Sechrest J, Lawrence TG, Van Etten J (1989) A phylogenetic analysis of the mycoplasmas: basis for their classification. J Bacteriol 171:6455–6467PubMedPubMedCentralCrossRefGoogle Scholar
  201. Westberg J, Persson A, Holmberg A, Goesmann A, Lundeberg J, Johansson K-E, Pettersson B, Uhlén M (2004) The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res 14:221–227PubMedPubMedCentralCrossRefGoogle Scholar
  202. Whitcomb RF, Tully JG, Bové JM, Bradbury JM, Christiansen G, Kahane I, Kirkpatrick BC, Laigret F, Leach RH, Neimark HC, Pollack JD, Razin S, Sears BB, Taylor-Robinson D (1995) Revised minimum standards for description of new species of the class Mollicutes (division Tenericutes). Int J Syst Bacteriol 45:605–612CrossRefGoogle Scholar
  203. Whitman WB (2015) Genome sequences as the type material for taxonomic descriptions of prokaryotes 1. Syst Appl Microbiol 38:217–222PubMedCrossRefGoogle Scholar
  204. Williamson DL, Gasparich GE, Regassa LB, Saillard C, Renaudin J, Bové JM, Whitcomb RF (2010) Family II. Spiroplasmataceae Skripal 1983, 408VP. In: Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology. The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes, vol 4. Springer, New York, pp 654–686Google Scholar
  205. Wolf M, Müller T, Dandekar T, Pollack JD (2004) Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int J Syst Evol Microbiol 54:871–875PubMedCrossRefGoogle Scholar
  206. Wong SY, Paschos A, Gupta RS, Schellhorn HE (2014) Insertion/deletion-based approach for the detection of Escherichia coli O157:H7 in freshwater environments. Environ Sci Technol 48:11462–11470PubMedCrossRefGoogle Scholar
  207. Wroblewski W (1931) Morphologie et cycle évolutif des microbes de la péripneumonie des bovidés et de l’agalaxie contagieuse des chèvres et des moutons. Ann Inst Pasteur 47:94–115Google Scholar
  208. Yamamoto R, Bigland CH, Ortmayer HB (1965) Characteristics of Mycoplasma meleagridis sp. n., isolated from turkeys. J Bacteriol 90:47–49PubMedPubMedCentralGoogle Scholar
  209. Yarza P, Richter M, Peplies J, Euzéby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R (2008) The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250PubMedCrossRefGoogle Scholar
  210. Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R (2010) Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299PubMedCrossRefGoogle Scholar
  211. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucl Acids Res 42:D643–D648PubMedCrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Radhey S. Gupta
    • 1
  • Sahil Sawnani
    • 1
  • Mobolaji Adeolu
    • 1
  • Seema Alnajar
    • 1
  • Aharon Oren
    • 2
  1. 1.Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada
  2. 2.Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life SciencesThe Hebrew University of JerusalemJerusalemIsrael

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