Promotion of Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris to species status

  • Christopher A. DunlapEmail author
  • Michael J. Bowman
  • Daniel R. Zeigler
Original Paper


Bacillus subtilis currently encompasses four subspecies, Bacillus subtilis subsp. subtilis, Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris. Several studies based on genomic comparisons have suggested these subspecies should be promoted to species status. Previously, one of the main reasons for leaving them as subspecies was the lack of distinguishing phenotypes. In this study, we used comparative genomics to determine the genes unique to each subspecies and used these to lead us to the unique phenotypes. The results show that one difference among the subspecies is they produce different bioactive secondary metabolites. B. subtilis subsp. spizizenii is shown conserve the genes to produce mycosubtilin, bacillaene and 3,3′-neotrehalosadiamine. B. subtilis subsp. inaquosorum is shown conserve the genes to produce bacillomycin F, fengycin and an unknown PKS/NRPS cluster. B. subtilis subsp. stercoris is shown conserve the genes to produce fengycin and an unknown PKS/NRPS cluster. While B. subtilis subsp. subtilis is shown to conserve the genes to produce 3,3′-neotrehalosadiamine. In addition, we update the chemotaxonomy and phenotyping to support their promotion to species status.


Core genome Secondary metabolites Antifungal Antibiotic Lipopeptide Surfactin Bacilysin Subtilosin 



The authors would like to thank Heather Walker for her technical expertise in genome sequencing and phenotype analysis. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture. The mention of firm names or trade products does not imply that they are endorsed or recommended by the USDA over other firms or similar products not mentioned. USDA is an equal opportunity provider and employer. This material is also based in part upon work supported by the National Science Foundation under Grant No. 1756219.

Author contributions

The study conception, design, comparative genomics and interpretation was performed by Christopher Dunlap. Mass spectroscopy and analysis was performed by Michael Bowman. Correlation of the genes to the Bacillus subtilis orthologs and associated interpretation the results was performed by Daniel Zeigler. The first draft of the manuscript was written by Christopher Dunlap and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.

Research involving human participants and/or animals

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

Supplementary material

10482_2019_1354_MOESM1_ESM.pdf (3 mb)
Supplementary material 1 (PDF 3112 kb)


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Copyright information

© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2019

Authors and Affiliations

  1. 1.Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research ServiceUnited States Department of AgriculturePeoriaUSA
  2. 2.Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research ServiceUnited States Department of AgriculturePeoriaUSA
  3. 3.Bacillus Genetic Stock CenterThe Ohio State UniversityColumbusUSA

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