Antonie van Leeuwenhoek

, Volume 112, Issue 12, pp 1725–1730 | Cite as

Genome-based reclassification 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

  • Guo-Hong Liu
  • Manik Prabhu Narsing Rao
  • Zhou-Yan Dong
  • Jie-Ping Wang
  • Jian-Mei Che
  • Qian-Qian Chen
  • Cetin Sengonca
  • Bo LiuEmail author
  • Wen-Jun LiEmail author
Original Paper


In the present study, phylogenetic and genome-based comparison was carried out to clarify the taxonomic positions of alkaliphilic Bacillus species, Bacillus plakortidis, Bacillus lehensis, Bacillus oshimensis, Bacillus rhizosphaerae and Bacillus clausii. Phylogenetic trees based on 16S rRNA gene sequences and concatenated protein marker genes were constructed. Average nucleotide identity (ANI) values were calculated to compare genetic relatedness. In phylogenetic trees, B. plakortidis DSM 19153T, B. lehensis DSM 19099T, and B. oshimensis DSM 18940T; B. rhizosphaerae DSM 21911T and B. clausii DSM 8716T clade together. The average nucleotide identity (ANI) values between B. oshimensis DSM 18940T, B. plakortidis DSM 19153T and B. lehensis DSM 19099T ranged from 98.7–98.8%, while the ANI values between B. rhizosphaerae DSM 21911T and B. clausii DSM 8716T were 95.2–95.5%. The ANI values were higher than the recognized threshold value for bacterial species delineation. Based on phylogenetic and genome comparison we propose reclassification of B. plakortidis and B. lehensis as a later heterotypic synonym of B. oshimensis; B. rhizosphaerae as a later heterotypic synonym of B. clausii.


Bacillus lehensis Bacillus oshimensis Bacillus plakortidis Bacillus rhizosphaerae Bacillus clausii Alkaliphilic Bacillus Phylogenomics Heterotypic synonym 



Average nucleotide identity



This work was financially supported by the External cooperative project of Fujian Academy of Agricultural Sciences (Grant No.: DEC201821209), the Science and Technology Innovation Team Program of Fujian Academy of Agricultural Sciences (Grant No.: STIT2017-1-11), The Scientific Research Foundation for Returned Scholars, Fujian Academy of Agricultural Sciences (Grant No.: YJRC2014-1).

Author’s contribution

GHL, MPNR, and ZYD performed genome analysis. JPW, JME, QQC performed the part of biochemical characterization. CS, GHL, and MPNR wrote the manuscript. BL and WJL supervised the experiments.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Agricultural Bio-resources Research InstituteFujian Academy of Agricultural SciencesFuzhouPeople’s Republic of China
  2. 2.State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life SciencesSun Yat-Sen UniversityGuangzhouPeople’s Republic of China
  3. 3.Institute of Crop Sciences and Resource Conservation (INRES)University of BonnBonnGermany
  4. 4.Key Laboratory of Biogeography and Bioresource in Arid LandXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesÜrümqiPeople’s Republic of China

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