Corrigendum to “Phylogenomic re-assessment of the thermophilic genus Geobacillus” [Syst. Appl. Microbiol. 39 (2016) 527–533] (Phylogenomic re-assessment of the thermophilic genus Geobacillus (2016) 39(8) (527–533), (S0723202016300959) (10.1016/j.syapm.2016.09.004));Phylogenomic re-assessment of the thermophilic genus Geobacillus

Systematic and Applied Microbiology

Volumn 39, Issue 8, 2016, Pages 527-533

  Aliyu, Habibu ^a   Lebre, Pedro ^a   Blom, Jochen ^b   Cowan, Don ^a   De Maayer, Pieter ^a  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Average Nucleotide Identity; Digital DNA DNA hybridization; Geobacillus; Phylogenomic metrics; Thermophile

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CLADISTICS; DNA DNA HYBRIDIZATION; GENE CLUSTER; GEOBACILLUS; MONOPHYLY; NONHUMAN; PHYLOGENOMICS; PHYLOGENY; PRIORITY JOURNAL; THERMOPHILIC BACTERIUM; CLASSIFICATION; DNA BASE COMPOSITION; GENETICS; MOLECULAR TYPING; NUCLEIC ACID HYBRIDIZATION;

BACTERIAL DNA; RNA 16S;

BASE COMPOSITION; DNA, BACTERIAL; GEOBACILLUS; MOLECULAR TYPING; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84992390987     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2018.07.001     Document Type: Erratum

References (55)

1. [1] Abd Rahman, R.N., Leow, T.C., Salleh, A.B., Basri, M., Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia. BMC Microbiol., 7, 2007, 77.
2. [2] 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, gkw255.
3. [3] Bosi, E., Donati, B., Galardini, M., Brunetti, S., Sagot, M.-F., et al. MeDuSa: a multi-draft based scaffolder. Bioinformatics 31 (2015), 2443–2451.
4. ® of Systematic Bacteriology, 2005, Springer, 27–32.
5. [5] Bryanskaya, A.V., Rozanov, A.S., Slynko, N.M., Shekhovtsov, S.V., Peltek, S.E., Geobacillus icigianus sp. nov., a thermophilic bacterium isolated from a hot spring. Int. J. Syst. Evol. Microbiol. 65 (2015), 864–869.
6. [6] Castresana, J., Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000), 540–552.
7. [7] Cole, J.R., Wang, Q., Fish, J.A., Chai, B., McGarrell, D.M., et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42 (2014), D633–D642.
8. [8] Coorevits, A., Dinsdale, A.E., Halket, G., Lebbe, L., De Vos, P., et al. Taxonomic revision of the genus Geobacillus: emendation of Geobacillus, G. stearothermophilus, G. jurassicus, G. toebii, G. thermodenitrificans and G. thermoglucosidans (nom. corrig. formerly ‘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. 62 (2012), 1470–1485.
9. [9] Darling, A.E., Mau, B., Perna, N.T., progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One, 5, 2010, e11147.
10. [10] Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23 (2007), 673–679.
11. [11] Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004), 1792–1797.
12. [12] Figueras, M.J., Beaz-Hidalgo, R., Hossain, M.J., Liles, M.R., Taxonomic affiliation of new genomes should be verified using average nucleotide identity and multilocus phylogenetic analysis. Genome Announc. 2 (2014), e00927–e009214.
13. [13] Fortina, M.G., Mora, D., Schumann, P., Parini, C., Manachini, P.L., Stackebrandt, E., Reclassification of Saccharococcus caldoxylosilyticus as Geobacillus caldoxylosilyticus (Ahmad et al. 2000) comb. nov. Int. J. Syst. Evol. Microbiol. 51 (2001), 2063–2071.
14. [14] Garcia-Vallvé, S., Palau, J., Romeu, A., Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol. Biol. Evol. 16 (1999), 1125–1134.
15. [15] Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., Tiedje, J.M., DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57 (2007), 81–91.
16. [16] Jenuth, J., The NCBI: publicly available tools and resources on the Web. Methods Mol. Biol. 132 (2000), 301–312.
17. [17] Kapralou, S., Fabbretti, A., Garulli, C., Gualerzi, C.O., Pon, C.L., Spurio, R., Characterization of Bacillus stearothermophilus infA and of its product IF1. Gene 428 (2009), 31–35.
18. [18] Katoh, K., Standley, D.M., MAFFT: iterative refinement and additional methods. Multiple Sequence Alignment Methods, 2014, Springer, 131–146.
19. [19] Kim, M., Oh, H.-S., Park, S.-C., 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. 64 (2014), 346–351.
20. [20] Konstantinidis, K., Tiedje, J., Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187 (2005), 6258–6264.
21. [21] Konstantinidis, K.T., Tiedje, J.M., Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U. S. A. 102 (2005), 2567–2572.
22. [22] Kuisiene, N., Raugalas, J., Chitavichius, D., Geobacillus lituanicus sp. nov. Int. J. Syst. Evol. Microbiol. 54 (2004), 1991–1995.
23. [23] Kuisiene, N., Raugalas, J., Chitavichius, D., Phylogenetic, inter, and intraspecific sequence analysis of spo0A gene of the genus Geobacillus. Curr. Microbiol. 58 (2009), 547–553.
24. [24] Lassmann, T., Sonnhammer, E.L., Kalign—an accurate and fast multiple sequence alignment algorithm. BMC Bioinform., 6, 2005, 298.
25. [25] Lerat, E., Daubin, V., Moran, N.A., From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol., 1, 2003, E19.
26. [26] Logan, N.A., Berge, O., Bishop, A.H., Busse, H.J., De Vos, P., et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int. J. Syst. Evol. Microbiol. 59 (2009), 2114–2121.
27. [27] MacLean, D., Jones, J.D., Studholme, D.J., Application of next-generation sequencing technologies to microbial genetics. Nat. Rev. Microbiol. 7 (2009), 287–296.
28. [28] Magis, C., Taly, J.-F., Bussotti, G., Chang, J.-M., Di Tommaso, P., et al. T-coffee: tree-based consistency objective function for alignment evaluation. Multiple Sequence Alignment Methods, 2014, Springer, 117–129.
29. [29] Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.-P., Göker, M., Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 14 (2013), 1–14.
30. [30] Meintanis, C., Chalkou, K.I., Kormas, K.A., Lymperopoulou, D.S., Katsifas, E.A., et al. Application of rpoB sequence similarity analysis, REP-PCR and BOX-PCR for the differentiation of species within the genus Geobacillus. Lett. Appl. Microbiol. 46 (2008), 395–401.
31. [31] Minana-Galbis, D., Pinzon, D.L., Loren, J.G., Manresa, A., Oliart-Ros, R.M., Reclassification of Geobacillus pallidus (Scholz et al. 1988) Banat et al. 2004 as Aeribacillus pallidus gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 60 (2010), 1600–1604.
32. [32] Nazina, T., Tourova, T., Poltaraus, A., Novikova, E., Grigoryan, A., 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, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Int. J. Syst. Evol. Microbiol. 51 (2001), 433–446.
33. [33] Nazina, T.N., Lebedeva, E.V., Poltaraus, A.B., Tourova, T.P., Grigoryan, A.A., 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. 54 (2004), 2019–2024.
34. [34] Nazina, T.N., Sokolova, D., Grigoryan, A.A., Shestakova, N.M., Mikhailova, E.M., et al. Geobacillus jurassicus sp. nov., a new thermophilic bacterium isolated from a high-temperature petroleum reservoir, and the validation of the Geobacillus species. Syst. Appl. Microbiol. 28 (2005), 43–53.
35. [35] Néron, B., Ménager, H., Maufrais, C., Joly, N., Maupetit, J., et al. Mobyle: a new full web bioinformatics framework. Bioinformatics 25 (2009), 3005–3011.
36. [36] 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. 42 (2014), D26–D31.
37. [37] Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 42 (2014), D206–D214.
38. [38] 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. 34 (2011), 419–423.
39. [39] Qin, Q.-L., Xie, B.-B., Zhang, X.-Y., Chen, X.-L., Zhou, B.-C., et al. A proposed genus boundary for the prokaryotes based on genomic insights. J. Bacteriol. 196 (2014), 2210–2215.
40. [40] Richter, M., Rosselló-Móra, R., Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U. S. A. 106 (2009), 19126–19131.
41. [41] Rodriguez-R, L.M., Konstantinidis, K.T. (2016). The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Rep. 2167-9843. PeerJ Preprints.
42. [42] Rossello-Mora, R., Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ. Microbiol. 14 (2012), 318–334.
43. [43] Smith, S.A., Dunn, C.W., Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 24 (2008), 715–716.
44. [44] Stackebrandt, E., Ebers, J., Taxonomic parameters revisited: tarnished gold standards. Microbiology Today, 2006, Microbiology Society, 152–155.
45. [45] Studholme, D.J., Some (bacilli) like it hot: genomics of Geobacillus species. Microbial Biotechnol. 8 (2015), 40–48.
46. [46] Sung, M.H., Kim, H., Bae, J.W., Rhee, S.K., Jeon, C.O., et al. Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost. Int. J. Syst. Evol. Microbiol. 52 (2002), 2251–2255.
47. [47] Sunna, A., Tokajian, S., Burghardt, J., Rainey, F., Antranikian, G., Hashwa, F., Identification of Bacillus kaustophilus, Bacillus thermocatenulatus and Bacillus strain HSR as members of Bacillus thermoleovorans. Syst. Appl. Microbiol. 20 (1997), 232–237.
48. [48] Talavera, G., Castresana, J., Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56 (2007), 564–577.
49. [49] Thompson, C.C., Amaral, G.R., Campeao, M., Edwards, R.A., Polz, M.F., et al. Microbial taxonomy in the post-genomic era: rebuilding from scratch?. Arch. Microbiol. 197 (2015), 359–370.
50. [50] Tindall, B.J., Rossello-Mora, R., Busse, H.J., Ludwig, W., Kampfer, P., Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60 (2010), 249–266.
51. [51] Vandamme, P., Peeters, C., Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 106 (2014), 57–65.
52. [52] Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F.O., Ludwig, W., et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat. Rev. Microbiol. 12 (2014), 635–645.
53. [53] Zeigler, D.R., Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 53 (2003), 1893–1900.
54. [54] Zeigler, D.R., Application of a recN sequence similarity analysis to the identification of species within the bacterial genus Geobacillus. Int. J. Syst. Evol. Microbiol. 55 (2005), 1171–1179.
55. [55] Zeigler, D.R., The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet?. Microbiology 160 (2014), 1–11.