1887

Abstract

Four novel strains of a member of the genus (Oakley, Holly, Lorelei and Ariel) were isolated from skin of Florida manatees (). These strains were phenotypically and genetically characterized and compared with the known species of the genera (.) (.), (.) (.) and (.). All the strains produced acid from glucose but did not hydrolyze arginine or urea. All were propagated in ambient air supplemented with 5±1 % CO at 35–37 °C using SP4-Z, Columbia and brain–heart infusion medium. Colonies on solid medium showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma-like cellular morphology. The results of phylogenetic analyses based on partial 16S rRNA, , and gene sequences and the whole proteome data indicated that the novel species is a unique species but phylogenetically closely related to , and ''. The average nucleotide identity and digital DNA–DNA hybridization values between strain Oakley and the closely related species were significantly lower than the accepted thresholds for describing novel prokaryotic species at the genomic level. On the basis of the genomic, phenotypic and phylogenetic properties, the novel strains represent a novel species of the genus , for which the name sp. nov. with the type strain Oakley (=NCTC 14352 =DSM 110686) is proposed. The genomic DNA G+C content and complete draft genome size for the type strain are 38.35 % and 1 873 856 bp, respectively.

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/content/journal/ijsem/10.1099/ijsem.0.005973
2023-07-25
2024-12-14
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References

  1. Watanabe M, Kojima H, Okano K, Fukui M. Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II-IV. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  2. Volokhov DV, Neverov AA, George J, Kong H, Liu SX et al. Genetic analysis of housekeeping genes of members of the genus Acholeplasma: phylogeny and complementary molecular markers to the 16S rRNA gene. Mol Phylogenet Evol 2007; 44:699–710 [View Article] [PubMed]
    [Google Scholar]
  3. Tully JG. Acholeplasmataceae. In Krieg NR, Holt JG. eds Bergey’s Manual of Systematic Bacteriology Baltimore: Williams & Wilkins; 1984 pp 775–781
    [Google Scholar]
  4. Razin S, Yogev D, Naot Y. Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 1998; 62:1094–1156 [View Article] [PubMed]
    [Google Scholar]
  5. Ayling RD, Bashiruddin SE, Nicholas RAJ. Mycoplasma species and related organisms isolated from ruminants in Britain between 1990 and 2000. Vet Rec 2004; 155:413–416 [View Article] [PubMed]
    [Google Scholar]
  6. Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. Phylum XVI. Tenericutes Murray 1984a, 356VP (Effective publication: Murray 1984b, 33.). In Bergey’s Manual of Systematic Bacteriology Springer; 2010 pp 567–723
    [Google Scholar]
  7. Brown DR, May M, Bradbury JM, Johansson K-E. Mollicutes. In Whitman WB. eds Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc; 2018
    [Google Scholar]
  8. Rogers MJ, Simmons J, Walker RT, Weisburg WG, Woese CR et al. Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data. Proc Natl Acad Sci U S A 1985; 82:1160–1164 [View Article] [PubMed]
    [Google Scholar]
  9. Merson SD, Ouwerkerk D, Gulino L-M, Klieve A, Bonde RK et al. Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida. FEMS Microbiol Ecol 2014; 87:601–615 [View Article] [PubMed]
    [Google Scholar]
  10. Sato T, Shibuya H, Ohba S, Nojiri T, Shirai W. Mycobacteriosis in two captive Florida manatees (Trichechus manatus latirostris). J Zoo Wildl Med 2003; 34:184–188 [View Article] [PubMed]
    [Google Scholar]
  11. Landsberg JH, Tabuchi M, Rotstein DS, Subramaniam K, Rodrigues TCS et al. Novel lethal clostridial infection in florida manatees (Trichechus manatus latirostris): cause of the 2013 unusual mortality event in the Indian river lagoon. Front Mar Sci 2022; 9: [View Article]
    [Google Scholar]
  12. Brown DR, Whitcomb RF, Bradbury JM. Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes). Int J Syst Evol Microbiol 2007; 57:2703–2719 [View Article] [PubMed]
    [Google Scholar]
  13. Firrao G, Brown DR. International committee on systematics of prokaryotes. subcommittee on the taxonomy of Mollicutes: minutes of the meetings, July 15th and 19th 2012, Toulouse, France. Int J Syst Evol Microbiol 2013; 63:2361–2364 [View Article] [PubMed]
    [Google Scholar]
  14. Brønstad A, Berg A-GT. The role of organizational culture in compliance with the principles of the 3Rs. Lab Anim 2011; 40:22–26 [View Article] [PubMed]
    [Google Scholar]
  15. Volokhov DV, Furtak VA, Blom J, Zagorodnyaya TA, Gao Y et al. Mycoplasma miroungirhinis sp. nov. and Mycoplasma miroungigenitalium sp. nov., isolated from northern elephant seals (Mirounga angustirostris), Mycoplasma phocoenae sp. nov., isolated from harbour porpoise (Phocoena phocoena), and Mycoplasma phocoeninasale sp. nov., isolated from harbour porpoise and California sea lions (Zalophus californianus). Int J Syst Evol Microbiol 2022; 72: [View Article]
    [Google Scholar]
  16. Volokhov DV, Gao Y, Davidson MK, Chizhikov VE. Acholeplasma equirhinis sp. nov. isolated from respiratory tract of horse (Equus caballus) and Mycoplasma procyoni sp. nov. isolated from oral cavity of raccoon (Procyon lotor). Arch Microbiol 2020; 202:411–420 [View Article] [PubMed]
    [Google Scholar]
  17. Harasawa R, Imada Y, Ito M, Koshimizu K, Cassell GH et al. Ureaplasma felinum sp. nov. and Ureaplasma cati sp. nov. isolated from the oral cavities of cats. Int J Syst Bacteriol 1990; 40:45–51 [View Article] [PubMed]
    [Google Scholar]
  18. Volokhov DV, Grózner D, Gyuranecz M, Ferguson-Noel N, Gao Y et al. Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology. Int J Syst Evol Microbiol 2020; 70:2369–2381 [View Article] [PubMed]
    [Google Scholar]
  19. Poveda JB. Biochemical characteristics in mycoplasma identification. Methods Mol Biol 1998; 104:69–78 [View Article] [PubMed]
    [Google Scholar]
  20. Volokhov DV, Gulland FM, Gao Y, Chizhikov VE. Ureaplasma miroungigenitalium sp. nov. isolated from northern elephant seals (Mirounga angustirostris) and Ureaplasma zalophigenitalium sp. nov. isolated from California sea lions (Zalophus californianus). Int J Syst Evol Microbiol 2020; 70:153–164 [View Article]
    [Google Scholar]
  21. Volokhov DV, Batac F, Gao Y, Miller M, Chizhikov VE. Mycoplasma enhydrae sp. nov. isolated from southern sea otters (Enhydra lutris nereis). Int J Syst Evol Microbiol 2019; 69:363–370 [View Article] [PubMed]
    [Google Scholar]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  23. McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004; 32:W20–5 [View Article] [PubMed]
    [Google Scholar]
  24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  25. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  26. Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE. 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 2012; 62:515–528 [View Article] [PubMed]
    [Google Scholar]
  27. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  28. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  29. Vannini C, Munz G, Mori G, Lubello C, Verni F et al. Sulphide oxidation to elemental sulphur in a membrane bioreactor: performance and characterization of the selected microbial sulphur-oxidizing community. Syst Appl Microbiol 2008; 31:461–473 [View Article] [PubMed]
    [Google Scholar]
  30. Deng Y, Zhang Y, Gao Y, Li D, Liu R et al. Microbial community compositional analysis for series reactors treating high level antibiotic wastewater. Environ Sci Technol 2012; 46:795–801 [View Article] [PubMed]
    [Google Scholar]
  31. Croese E, Pereira MA, Euverink G-JW, Stams AJM, Geelhoed JS. Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell. Appl Microbiol Biotechnol 2011; 92:1083–1093 [View Article] [PubMed]
    [Google Scholar]
  32. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 2020; 70:e102 [View Article] [PubMed]
    [Google Scholar]
  33. Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S et al. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database 2016; 2016:baw022 [View Article] [PubMed]
    [Google Scholar]
  34. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  35. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  36. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  37. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  38. Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 2006; 361:1929–1940 [View Article] [PubMed]
    [Google Scholar]
  39. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
    [Google Scholar]
  40. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  41. Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 2003; 13:145–158 [View Article] [PubMed]
    [Google Scholar]
  42. Teeling H, Meyerdierks A, Bauer M, Amann R, Glöckner FO. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 2004; 6:938–947 [View Article] [PubMed]
    [Google Scholar]
  43. Medlar AJ, Törönen P, Holm L. AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 2018; 46:W479–W485 [View Article] [PubMed]
    [Google Scholar]
  44. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  45. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  46. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  47. Gasparich GE, Kuo CH. Genome analysis-based union of the genus Mesoplasma with the genus Entomoplasma. Int J Syst Evol Microbiol 2019; 69:2735–2738 [View Article]
    [Google Scholar]
  48. Furuno M, Kasukawa T, Saito R, Adachi J, Suzuki H et al. CDS annotation in full-length cDNA sequence. Genome Res 2003; 13:1478–1487 [View Article] [PubMed]
    [Google Scholar]
  49. Liu B, Zheng D, Jin Q, Chen L, Yang J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019; 47:D687–D692 [View Article] [PubMed]
    [Google Scholar]
  50. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA et al. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 2013; 57:3348–3357 [View Article] [PubMed]
    [Google Scholar]
  51. Pollack JD, Williams MV, McElhaney RN. The comparative metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells. Crit Rev Microbiol 1997; 23:269–354 [View Article] [PubMed]
    [Google Scholar]
  52. O’Brien SJ, Simonson JM, Razin S, Barile MF. On the distribution and characteristics of isozyme expression in Mycoplasma, Acholeplasma, and Ureaplasma species. Yale J Biol Med 1983; 56:701–708 [PubMed]
    [Google Scholar]
  53. O’Brien SJ, Simonson JM, Grabowski MW, Barile MF. Analysis of multiple isoenzyme expression among twenty-two species of Mycoplasma and Acholeplasma. J Bacteriol 1981; 146:222–232 [View Article] [PubMed]
    [Google Scholar]
  54. Meier B, Habermehl GG. Evidence for superoxide dismutase and catalase in mollicutes and release of reactive oxygen species. Arch Biochem Biophys 1990; 277:74–79 [View Article] [PubMed]
    [Google Scholar]
  55. Kämpfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited. Environ Microbiol 2012; 14:291–317 [View Article] [PubMed]
    [Google Scholar]
  56. Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J et al. Microbiome composition and function in aquatic vertebrates: small organisms making big impacts on aquatic Animal health. Front Microbiol 2021; 12:567408 [View Article] [PubMed]
    [Google Scholar]
  57. Apprill A, Miller CA, Van Cise AM, U’Ren JM, Leslie MS et al. Marine mammal skin microbiotas are influenced by host phylogeny. R Soc Open Sci 2020; 7:192046 [View Article] [PubMed]
    [Google Scholar]
  58. Egerton S, Culloty S, Whooley J, Stanton C, Ross RP. The gut microbiota of marine fish. Front Microbiol 2018; 9:873 [View Article] [PubMed]
    [Google Scholar]
  59. Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl Environ Microbiol 2011; 77:1153–1161 [View Article] [PubMed]
    [Google Scholar]
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