1887

Abstract

Members of the genus within the phylum are Gram-stain-positive, aerobic, endospore-forming, obligate thermophiles. In 2016, the genus was subdivided into two genera based on whole-genome approaches. The new genus, , comprises five genomospecies. In this study, we recommend the reclassification of two species, and , into the genus . We have applied whole genome approaches to estimate the phylogenetic relatedness among the 18 and type strains for which genome sequences are currently publicly available. The phylogenomic metrics AAI (average amino acid identity), ANI (average nucleotide identity) and dDDH (digital DNA–DNA hybridization) denoted that the type strains of and belong to the genus . Furthermore, a phylogeny based on comparison of the 16S rRNA gene sequences, gene sequences and core genes identified from the whole-genome analyses designated that the type strains of and belong in the genus . With these findings, we consequently propose that and should be reclassified as comb. nov. and comb. nov.

Funding
This study was supported by the:
  • Department of Biotechnology, Ministry of Science & Technology, Government of India (Award DBT-NER/Health/45/2015 & BT/PR25092/NER/95/1009/2017)
    • Principle Award Recipient: Nagendra Thakur
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2020-11-09
2024-05-04
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References

  1. Nazina TN, Tourova TP, Poltaraus AB, Novikova EV, Grigoryan AA et al. Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillusthermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G.thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans . Int J Syst Evol Microbiol 2001; 51:433–446 [View Article]
    [Google Scholar]
  2. An C, Dinsdale AE, Halket G, Lebbe L, De VP et al. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidasius (nom.corrig., formaly ‘thermoglucosidasius’); transfer of Bacillus thermantarcticus to the genus as G. thermantarcticus comb. nov.; proposal of Caldibacillus debilis gen. nov., comb. nov.; transfer of G. tepidamans to Anoxybacillus as A. tepidamans comb. nov.; and proposal of Anoxybacillus caldiproteolyticus sp. nov.. Int J Syst Evol Microbiol 2012; 62:1470–1485
    [Google Scholar]
  3. Kuisiene N, Raugalas J, Chitavichius D. Geobacillus lituanicus sp. nov. Int J Syst Evol Microbiol 2004; 54:1991–1995 [View Article]
    [Google Scholar]
  4. Maugeri TL, Gugliandolo C, Caccamo D, Stackebrandt E. Three novel halotolerant and thermophilic Geobacillus strains from shallow marine vents. Syst Appl Microbiol 2002; 25:450–455 [View Article]
    [Google Scholar]
  5. Popova NA, Nikolaev YA, Tourova TP, Lysenko AM, Osipov GA et al. Geobacillus uralicus, a new species of thermophilic bacteria. Microbiology 2002; 71:335–341 [View Article]
    [Google Scholar]
  6. Hawumba JF, Theron J, Brözel VS. Thermophilic protease-producing Geobacillus from Buranga hot springs in western Uganda. Curr Microbiol 2002; 45:144–150 [View Article]
    [Google Scholar]
  7. Nazina TN, Lebedeva EV, Poltaraus AB, Tourova TP, Grigoryan AA et al. Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Int J Syst Evol Microbiol 2004; 54:2019–2024 [View Article]
    [Google Scholar]
  8. Takami H, Nishi S, Lu J, Shimamura S, Takaki Y. Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench. Extremophiles 2004; 8:351–356 [View Article]
    [Google Scholar]
  9. Sung M, Kim H, Bae J, Rhee S, Jeon CO et al. Geobacillus toebii sp. nov. a novel thermophilic bacterium isolated from hay compost; 2016; 522251–2255
  10. Wiegand S, Rabausch U, Chow J, Daniel R, Streit WR et al. Complete genome sequence of Geobacillus sp. Strain GHH01, a thermophilic lipase-secreting bacterium. Genome Announc 2013; 1:1–2 [View Article]
    [Google Scholar]
  11. Ash C, Farrow JAE, Wallbanks S, Collins MD. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 1991; 13:202–206 [View Article]
    [Google Scholar]
  12. Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P, De MP. Phylogenomic re-assessment of the thermophilic genus Geobacillus . Syst Appl Microbiol 2016; 39:527–533 [View Article]
    [Google Scholar]
  13. Aliyu H, Lebre P, Blom J, Cowana D, De MP. Corrigendum to “Phylogenomic re-assessment of the thermophilic genus Geobacillus” [Syst Appl. Microbiol. 39 (2016) 527–533]. Syst Appl Microbiol 2018; 41:529–530
    [Google Scholar]
  14. Zeigler DR. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 2003; 53:1893–1900 [View Article]
    [Google Scholar]
  15. Kumar A, Prameela TP, Suseelabhai R. A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences. J Biosci 2013; 38:267–278 [View Article][PubMed]
    [Google Scholar]
  16. Vandamme P, Peeters C. Time to revisit polyphasic taxonomy. Antonie van Leeuwenhoek 2014; 106:57–65 [View Article]
    [Google Scholar]
  17. 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]
    [Google Scholar]
  18. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  19. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  20. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–14 [View Article]
    [Google Scholar]
  21. Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P et al. Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Microbiol 2008; 58:200–214 [View Article]
    [Google Scholar]
  22. Glazunova OO, Raoult D, Roux V. Partial recN gene sequencing: a new tool for identification and phylogeny within the genus Streptococcus . Int J Syst Evol Microbiol 2010; 60:2140–2148 [View Article]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  24. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A et al. The genome portal of the Department of energy joint genome Institute: 2014 updates. Nucleic Acids Res 2014; 42:D26–D31 [View Article]
    [Google Scholar]
  25. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
    [Google Scholar]
  26. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [View Article]
    [Google Scholar]
  27. Lerat E, Daubin V, Moran NA. From gene trees to organismal phylogeny in prokaryotes:The case of the γ-Proteobacteria. PLoS Biol 2003; 1:e19–109 [View Article]
    [Google Scholar]
  28. Edgar RC. Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113–119 [View Article]
    [Google Scholar]
  29. Retief JD. Phylogenetic analysis using PHYLIP. Methods Mol Biol 2000; 132:243–258
    [Google Scholar]
  30. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490–10 [View Article]
    [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. MolecBiolEvol 1987; 4:406–425
    [Google Scholar]
  32. Jin G, Nakhleh L, Snir S, Tuller T. Maximum likelihood of phylogenetic networks. Bioinformatics 2006; 22:2604–2611 [View Article]
    [Google Scholar]
  33. Kannan L, Wheeler WC. Maximum parsimony on phylogenetic networks. Algorithms Mol Biol 2012; 7:1–10 [View Article]
    [Google Scholar]
  34. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10: [View Article]
    [Google Scholar]
  35. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast Distance-Based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article]
    [Google Scholar]
  36. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
  37. Kreft Łukasz, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 2017; 33:2946–2947 [View Article]
    [Google Scholar]
  38. Zeigler DR. Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus . Int J Syst Evol Microbiol 2005; 55:1171–1179 [View Article]
    [Google Scholar]
  39. Studholme DJ. Genomics update Some (bacilli) like it hot : genomics of Geobacillus species. Microb Biotechnol 2015; 8:40–48
    [Google Scholar]
  40. Poli A, Laezza G, Gul-Guven R, Orlando P, Nicolaus B. Geobacillus galactosidasius sp. nov., a new thermophilic galactosidase-producing bacterium isolated from compost. Syst Appl Microbiol 2011; 34:419–423 [View Article]
    [Google Scholar]
  41. Ramaloko WT, Nadine K, Shamara P, Habibu A, Pedro HL et al. High quality draft genomes of the type strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T . J Genomics 2018; 6:20–23
    [Google Scholar]
  42. Najar IN, Sherpa MT, Das S, Verma K, Dubey VK et al. Geobacillus yumthangensis sp. nov., a thermophilic bacterium isolated from a north-east Indian hot spring. Int J Syst Evol Microbiol 2018; 68:3430–3434 [View Article]
    [Google Scholar]
  43. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  44. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687
    [Google Scholar]
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