1887

Abstract

Chemotaxonomic parameters, phylogenetic analysis of the 16S rRNA gene, phylogenetic analysis of 90 housekeeping genes and 855 core genes, amino acid identity (AAI), average nucleotide identity (ANI) and genomic characteristics were used to examine the 13 species of the genus with validly published names to reclassify this genus. The results indicate that the species of the genus can be divided into three lineages on the basis of the results of the phylogenetic analysis, AAI, the guanine+cytosine (G+C) mole ratio, the ability to synthesize the red-pigmented carotenoid canthaxanthin and the colony colour, as well as other genomic characteristics. The results presented in this study circumscribe the genus to the species , , , , , , and , for which it is necessary to emend the genus . The species , which clearly represents a separate genus level lineage was not reclassified in this study for lack of any distinctive phenotypic or genotypic characteristics. The results of this study led us to reclassify the species , , and as species of a novel genus for which we propose the epithet gen. nov.

Funding
This study was supported by the:
  • Horizon 2020 Research and Innovation (Award 685474)
  • Compete 2020 (Award UID/NEU/04539/2013)
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2019-02-11
2024-03-29
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References

  1. Nobre MF, Truper HG, da Costa MS. Transfer of Thermus ruber (Loginova et al. 1984), Thermus silvanus (Tenreiro et al. 1995), and Thermus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb. nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus . Int J Syst Bacteriol 1996; 46:604–606 [View Article]
    [Google Scholar]
  2. Loginova LG, Egorova LA, Golovacheva RS, Seregina LM. Thermus ruber sp. nov., nom. rev. Int J Syst Bacteriol 1984; 34:498–499 [View Article]
    [Google Scholar]
  3. Tenreiro S, Nobre MF, da Costa MS. Thermus silvanus sp. nov. and Thermus chliarophilus sp. nov., two new species related to Thermus ruber but with lower growth temperatures. Int J Syst Bacteriol 1995; 45:633–639 [View Article][PubMed]
    [Google Scholar]
  4. Chung AP, Rainey F, Nobre MF, Burghardt J, da Costa MS. Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids. Int J Syst Bacteriol 1997; 47:1225–1230 [View Article][PubMed]
    [Google Scholar]
  5. Chen MY, Lin GH, Lin YT, Tsay SS. Meiothermus taiwanensis sp. nov., a novel filamentous, thermophilic species isolated in Taiwan. Int J Syst Evol Microbiol 2002; 52:1647–1654 [View Article][PubMed]
    [Google Scholar]
  6. Pires AL, Albuquerque L, Tiago I, Nobre MF, Empadinhas N et al. Meiothermus timidus sp. nov., a new slightly thermophilic yellow-pigmented species. FEMS Microbiol Lett 2005; 245:39–45 [View Article][PubMed]
    [Google Scholar]
  7. Albuquerque L, Ferreira C, Tomaz D, Tiago I, Veríssimo A et al. Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus . Syst Appl Microbiol 2009; 32:306–313 [View Article][PubMed]
    [Google Scholar]
  8. Zhang XQ, Zhang WJ, Wei BP, Xu XW, Zhu XF et al. Meiothermus cateniformans sp. nov., a slightly thermophilic species from north-eastern China. Int J Syst Evol Microbiol 2010; 60:840–844 [View Article][PubMed]
    [Google Scholar]
  9. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Meiothermus granaticius sp. nov., a new slightly thermophilic red-pigmented species from the Azores. Syst Appl Microbiol 2010; 33:243–246 [View Article][PubMed]
    [Google Scholar]
  10. Mori K, Iino T, Ishibashi J, Kimura H, Hamada M et al. Meiothermus hypogaeus sp. nov., a moderately thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2012; 62:112–117 [View Article][PubMed]
    [Google Scholar]
  11. Yu TT, Yin YR, Zhang YG, Yao JC, Klenk HP et al. Meiothermus terrae sp. nov., isolated from a geothermally heated soil sample. Int J Syst Evol Microbiol 2014; 64:794–798 [View Article][PubMed]
    [Google Scholar]
  12. Ming H, Duan YY, Guo QQ, Yin YR, Zhou EM et al. Meiothermus roseus sp. nov., a thermophilic bacterium isolated from a geothermal area. Antonie van Leeuwenhoek 2015; 108:897–905 [View Article][PubMed]
    [Google Scholar]
  13. Habib N, Khan IU, Hussain F, Zhou E-M, Xiao M et al. Meiothermus luteus sp. nov., a slightly thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:2910–2914 [View Article][PubMed]
    [Google Scholar]
  14. Albuquerque L, Rainey FA, da Costa MS. Meiothermus. In Whitman WB. (editor) Bergey's Manual of Systematics of Archaea and Bacteria vol. 28 John Wiley & Sons, Inc: in association with Bergey's Manual Trust; 2018 pp. 1–28
    [Google Scholar]
  15. Albuquerque L, da Costa MS. Family Thermaceae. In DeLong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes-Other Major Lineages of Bacteria and The Archaea, 4th ed. Berlin Heidelberg: Springer-Verlag; 2014 pp. 955–987
    [Google Scholar]
  16. Miroshnichenko ML, L´Haridon S, Jeanthon C, Antipov AN, Kostrikina NA et al. Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2003; 53:747–752 [View Article][PubMed]
    [Google Scholar]
  17. Miroshnichenko ML, L´Haridon S, Nercessian O, Antipov AN, Kostrikina NA et al. Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 2003; 53:1143–1148 [View Article][PubMed]
    [Google Scholar]
  18. Mori K, Kakegawa T, Higashi Y, Nakamura K, Maruyama A et al. Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount. Int J Syst Evol Microbiol 2004; 54:1561–1566 [View Article][PubMed]
    [Google Scholar]
  19. Sako Y, Nakagawa S, Takai K, Horikoshi K. Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2003; 53:59–65 [View Article][PubMed]
    [Google Scholar]
  20. Steinsbu BO, Tindall BJ, Torsvik VL, Thorseth IH, Daae FL et al. Rhabdothermus arcticus gen. nov., sp. nov., a member of the family Thermaceae isolated from a hydrothermal vent chimney in the Soria Moria vent field on the Arctic Mid-Ocean Ridge. Int J Syst Evol Microbiol 2011; 61:2197–2204 [View Article][PubMed]
    [Google Scholar]
  21. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. In Rainey FA, Oren A. (editors) Methods in Microbiology (Taxonomy of Prokaryotes) vol. 38 London: Elsevier Ltd; 2011 pp. 165–181
    [Google Scholar]
  22. da Costa MS, Albuquerque L, Nobre MF, Wait R, Oren A et al. The identification of fatty acids in bacteria. In Rainey FA. (editor) Methods in Microbiology (Taxonomy of Prokaryotes) vol. 38 London: Elsevier Ltd; 2011 pp. 183–196
    [Google Scholar]
  23. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995; 141:1745–1761 [View Article]
    [Google Scholar]
  24. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  26. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
    [Google Scholar]
  27. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  28. Apweiler R, Bairoch A, Ch W, Barker WC, Boeckmann B et al. UniProt: the universal protein knowledgebase. Nucleic Acids Res 2017; 45:D115–D119 [View Article][PubMed]
    [Google Scholar]
  29. Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G et al. HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res 2015; 43:D1064–D1070 [View Article][PubMed]
    [Google Scholar]
  30. Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003; 31:371–373 [View Article][PubMed]
    [Google Scholar]
  31. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–D285 [View Article][PubMed]
    [Google Scholar]
  32. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  33. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  34. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188–7196 [View Article][PubMed]
    [Google Scholar]
  35. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  36. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
    [Google Scholar]
  37. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic tress. Mol Bio. Evol 1987; 4:406–425
    [Google Scholar]
  38. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  39. Viver T, Orellana L, González-Torres P, Díaz S, Urdiain M et al. Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano. Syst Appl Microbiol 2018; 41:198–212 [View Article][PubMed]
    [Google Scholar]
  40. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article][PubMed]
    [Google Scholar]
  41. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  42. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J. Preprints 2016:e1900v1
    [Google Scholar]
  43. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  44. Wickham H. ggplot2: Elegant Graphics for Data Analysis Springer-Verlag New York; 2016
    [Google Scholar]
  45. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  46. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea . Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
    [Google Scholar]
  47. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  48. Ferreira AM, Wait R, Nobre MF, da Costa MS. Characterization of glycolipids from Meiothermus spp. Microbiology 1999; 145:1191–1199 [View Article][PubMed]
    [Google Scholar]
  49. Carreto L, Wait R, Nobre MF, da Costa MS. Determination of the structure of a novel glycolipid from Thermus aquaticus 15004 and demonstration that hydroxy fatty acids are amide linked to glycolipids in Thermus spp. J Bacteriol 1996; 178:6479–6486 [View Article][PubMed]
    [Google Scholar]
  50. Lagutin K, Mackenzie A, Houghton KM, Stott MB, Vyssotski M. The identification and quantification of phospholipids from Thermus and Meiothermus bacteria. Lipids 2014; 49:1133–1141 [View Article][PubMed]
    [Google Scholar]
  51. Yang YL, Yang FL, Jao SC, Chen MY, Tsay SS et al. Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus . J Lipid Res 2006; 47:1823–1832 [View Article][PubMed]
    [Google Scholar]
  52. Wait R, Carreto L, Nobre MF, Ferreira AM, da Costa MS. Characterization of novel long-chain 1,2-diols in Thermus species and demonstration that Thermus strains contain both glycerol-linked and diol-linked glycolipids. J Bacteriol 1997; 179:6154–6162 [View Article][PubMed]
    [Google Scholar]
  53. Burgess ML, Barrow KD, Gao C, Heard GM, Glenn D. Carotenoid glycoside esters from the thermophilic bacterium Meiothermus ruber . J Nat Prod 1999; 62:859–863 [View Article][PubMed]
    [Google Scholar]
  54. Mukherjee T, Bose S, Sen U, Roy C, Rameez MJ et al. Genome sequence of the red pigment-forming Meiothermus taiwanensis strain RP isolated from Paniphala hot spring, India. Genome Announc 2016; 4:e0062916 [View Article][PubMed]
    [Google Scholar]
  55. Kim SH, Park YH, Schmidt-Dannert C, Lee PC. Redesign, reconstruction, and directed extension of the Brevibacterium linens C40 carotenoid pathway in Escherichia coli . Appl Environ Microbiol 2010; 76:5199–5206 [View Article][PubMed]
    [Google Scholar]
  56. Yokoyama A et al. Thermozeaxanthins, new carotenoid-glycoside-esters from thermophilic eubacterium Thermus thermophilus . Tetrahedron Lett 1995; 36:4901–4904 [View Article]
    [Google Scholar]
  57. Boos W, Shuman H. Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation. Microbiol Mol Biol Rev 1998; 62:204–229[PubMed]
    [Google Scholar]
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