Genome-Based Reclassification of Anoxybacillus geothermalis Filippidou et al. 2016 as a Later Heterotypic Synonym of Anoxybacillus rupiensis Derekova et al. 2007

Pikuta E, Lysenko A, Chuvilskaya N, Mendrock U et al (2000) Anoxybacillus pushchinensis gen. nov., sp. nov., a novel anaerobic, alkaliphilic, moderately thermophilic bacterium from manure, and description of Anoxybacillus flavithermus comb. nov. Int J Syst Evol Microbiol 50:2109–2117. https://doi.org/10.1099/00207713-50-6-2109

Article  CAS  PubMed  Google Scholar 

Pikuta E, Cleland D, Tang J (2003) Aerobic growth of Anoxybacillus pushchinoensis K1T: emended descriptions of A. pushchinoensis and the genus Anoxybacillus. Int J Syst Evol Microbiol 53:1561–1562. https://doi.org/10.1099/ijs.0.02643-0

Article  CAS  PubMed  Google Scholar 

Liu GH, Rao MPN, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJ (2019) Genome-based reclassifcation of Bacillus plakortidis Borchert et al. 2007 and Bacillus lehensis Ghosh et al. 2007 as a later heterotypic synonym of Bacillus oshimensis Yumoto et al. 2005; Bacillus rhizosphaerae Madhaiyan et al. 2011 as a later heterotypic synonym of Bacillus clausii Nielsen et al. 1995. Anton Leeuw 112:1725–1730. https://doi.org/10.1007/s10482-019-01299-z

Article  CAS  Google Scholar 

Rao MPN, Xiao M, Liu D, Tang R, Liu G, Li W (2022) Genome-based reclassifcation of Evansella polygoni as a later heterotypic synonym of Evansella clarkii and transfer of Bacillus shivajii and Bacillus tamaricis to the genus Evansella as Evansella shivajii comb. nov. and Evansella tamaricis comb. nov. Arch Microbiol 204:47. https://doi.org/10.1007/s00203-021-02720-w

Article  CAS  Google Scholar 

Derekova A, Sjøholm C, Mandeva R, Kambourova M (2007) Anoxybacillus rupiensis sp. nov., a novel thermophilic bacterium isolated from Rupi basin (Bulgaria). Extremophiles 11:577–583. https://doi.org/10.1007/s00792-007-0071-4

Article  PubMed  Google Scholar 

Euzeby JP (2008) Validation list no. 119. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 58:1–2

Filippidou S, Jaussi M, Junier T et al (2016) Anoxybacillus geothermalis sp. nov., a facultatively anaerobic, endospore-forming bacterium isolated from mineral deposits in a geothermal station. Int J Syst Evol Microbiol 66:2944–2951. https://doi.org/10.1099/ijsem.0.001125

Article  CAS  PubMed  Google Scholar 

Wattam AR, Davis JJ, Assaf R et al (2017) Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acid Res 45:D535–D542. https://doi.org/10.1093/nar/gkw1017

Article  CAS  PubMed  Google Scholar 

Aziz RK, Bartels D, Best AAB et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98. https://doi.org/10.14601/Phytopathol_Mediterr-14998u1.29

Article  CAS  Google Scholar 

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680. https://doi.org/10.1093/nar/22.22.4673

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/bf01731581

Article  ADS  CAS  PubMed  Google Scholar 

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

Article  CAS  PubMed  Google Scholar 

Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/bf01734359

Article  ADS  CAS  PubMed  Google Scholar 

Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10(1):2182. https://doi.org/10.1038/s41467-019-10210-3

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60

Article  PubMed  PubMed Central  Google Scholar 

Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66(2):1100–1103. https://doi.org/10.1099/ijsem.0.000760

Article  CAS  PubMed  Google Scholar 

Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Anton Leeuw 110(10):1281–2128. https://doi.org/10.1007/s10482-017-0844-4

Article  CAS  Google Scholar 

Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153

Article  CAS  PubMed  Google Scholar 

Price MN, Dehal PS, Arkin AP (2010) FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. https://doi.org/10.1371/journal.pone.0009490

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Arkin AP, Cottingham RW, Henry CS et al (2018) KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 36:566–569. https://doi.org/10.1038/nbt.4163

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identifcation of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189. https://doi.org/10.1101/gr.1224503

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tindall BJ (1990) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130. https://doi.org/10.1016/S0723-2020(11)80158-X

Article  CAS  Google Scholar 

Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202. https://doi.org/10.1016/0378-1097(90)90282-U

Article  CAS  Google Scholar 

Tindall BJ, Sikorski J, Smibert RM, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology, 3rd edn. American Society for Microbiology, Washington, DC, pp 330–393. https://doi.org/10.1128/9781555817497.ch15

Chapter  Google Scholar 

Collins MD (1985) Analysis of isoprenoid quinones. Methods Microbiol 18:329–366. https://doi.org/10.1016/S0580-9517(08)70480-X

Article  CAS  Google Scholar 

Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY (2018) Phylogenomic analysis of the gammaproteobacterial methanotrophs (order methylococcales) calls for the reclassification of members at the genus and species levels. Front Microbiol 9:3162. https://doi.org/10.3389/fmicb.2018.03162

Article  PubMed  PubMed Central  Google Scholar 

Wayne LG, Brenner DJ, Colwell RR et al (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464. https://doi.org/10.1016/s0176-6724(88)80120-2

Article  Google Scholar 

Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 06(45):19126–19131. https://doi.org/10.1073/pnas.0906412106

Article  ADS  Google Scholar 

Luo C, Rodriguez-R LM, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42(8):e73. https://doi.org/10.1093/nar/gku169

Article  CAS  PubMed  PubMed Central  Google Scholar 

Parker CT, Tindall BJ, Garrity GM (2019) International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 69(1A):S1–S111. https://doi.org/10.1099/ijsem.0.000778

Article  Google Scholar 

Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 32:2798–2800. https://doi.org/10.1093/molbev/msv150

Article  CAS  PubMed  PubMed Central  Google Scholar 

Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106(951):645–667. https://doi.org/10.1086/282802

Article  Google Scholar 

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