An investigation into the taxonomy of “Bacillus aminovorans” and its reclassification to the genus Domibacillus as Domibacillus aminovorans sp. nov.☆

https://doi.org/10.1016/j.syapm.2017.07.003Get rights and content

Abstract

The species “Bacillus aminovorans” was categorized as species Incertae Sedis meaning taxa with uncertain taxonomic position because of insufficient description of phenotypic properties and lack of understanding of its phylogenetic relationship (Claus and Berkeley [5]). In this study two strains “B. aminovorans” DSM 1314T and DSM 4337 were phenotypically and phylogenomically analyzed. The strains are Gram-staining-positive, spore forming rods and unable to utilize/ferment most of the sugars tested except glucose. The major fatty acids are anteiso-C15:0 and iso-C15:0. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and an aminophosphoglycolipid. The cell wall peptidoglycan is of A1γ type with meso-Dpm as the diamino acid. The menaquinone type present is MK-6. The G + C content of the genomic DNA of the type strain is 40.8 mol%. These characteristics were found to be in line with description of the genus Domibacillus. Moreover phylogenetic analysis based on 16S rRNA gene sequence retrieved “B. aminovorans” within the genus Domibacillus with D. antri XD 80T as the closest relative. Additionally genome sequencing of the strains and their comparison with whole genome sequences of other Domibacillus spp. confirmed their distinctiveness and separate species status within the genus based on parameters of genome to genome distance calculator (GGDC) and average nucleotide identity (ANI) values. Therefore a novel species Domibacillus aminovorans sp. nov. (DSM 1314T = LMG 16796T) is proposed.

Section snippets

Acknowledgements

We are thankful to Mr. Deepak and Mr. Paramjit for their help in DNA sequencing and MALDI-TOF experiments. This work was supported by the project “Use of genomic approaches in deciphering taxonomic intricacies in bacterial taxa (OLP0114)”. AV and YP are recipients of CSIR and UGC fellowship respectively. PK worked in MTCC project jointly funded by CSIR and DBT (Expansion and modernization of Microbial Type Culture Collection and Gene Bank (MTCC) jointly supported by Council of Scientific and

References (55)

  • F. Allerberger et al.

    Use of automated ribotyping of Austrian Listeria monocytogenes isolates to support epidemiological typing

    J. Microbiol. Methods

    (1999)
  • R. Rosselló-Móra et al.

    The species concept for prokaryotes

    FEMS Microbiol. Rev.

    (2001)
  • P. Schumann

    Peptidoglycan structure

    Methods Microbiol.

    (2011)
  • R.A. Albert et al.

    Proposal of Viridibacillus gen. nov. and reclassification of Bacillus arvi, Bacillus arenosi and Bacillus neidei as Viridibacillus arvi gen. nov., comb. nov., Viridibacillus arenosi comb. nov. and Viridibacillus neidei comb. nov

    Int. J. Syst. Evol. Microbiol.

    (2007)
  • C. Ash et al.

    Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus

    Antonie van Leeuwenhoek

    (1993)
  • E.G. Bligh et al.

    A rapid method of total lipid extraction and purification

    Can. J. Biochem. Physiol.

    (1959)
  • D. Claus et al.

    Genus Bacillus Cohn 1872

  • M.D. Collins et al.

    Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diamino butyric acid (DAB)

    J. Appl. Bacteriol.

    (1980)
  • den Dooren de Jong, L.E. (1927) Über protaminophage Bakterien Zentralbl. Bakteriol. Parasitenkd. Abt. II 71,...
  • J.A. Farrow et al.

    Phylogenetic interrelationships of round-spore-forming bacilli containing cell walls based on lysine and the non-spore-forming genera Caryophanon, Exiguobacterium, Kurthia, and Planococcus

    Int. J. Syst. Bacteriol.

    (1994)
  • J. Felsentein

    Confidence limits on phylogenies: an approach using the bootstrap

    Evolution

    (1985)
  • R.S. Golovacheva et al.

    New thermophilic species, Bacillus thermocatenulatus nov. sp

    Microbiology

    (1975)
  • J. Goris et al.

    DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

    Int. J. Syst. Evol. Microbiol.

    (2007)
  • H.R. Gyeong et al.

    Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus

    Int. J. Syst. Evol. Microbiol.

    (2015)
  • M. Heyndrickx et al.

    A polyphasic reassessment of the genus Aneurinibacillus, reclassification of Bacillus thermoaerophilus (Meier-Stauffer et al. 1996) as Aneurinibacillus thermoaerophilus comb. nov, and emended descriptions of A. aneurinilyticus corrig., A. migulanus, and A. thermoaerophilus

    Int. J. Syst. Bacteriol.

    (1997)
  • M. Heyndrickx et al.

    Reclassification of Paenibacillus (formerly Bacillus) pulvifaciens (Nakamura 1984) Ash et al. 1994, a later subjective synonym of Paenibacillus (formerly Bacillus) larvae (White 1906) Ash et al. 1994, as a subspecies of P. larvae, with emended descriptions of P. larvae as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens

    Int. J. Syst. Bacteriol.

    (1996)
  • O.S. Kim et al.

    Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

    Int. J. Syst. Evol. Microbiol.

    (2012)
  • K. Komagata et al.

    Lipid and cell-wall analysis in bacterial systematics

    Methods Microbiol.

    (1987)
  • S. Krishnamurthi et al.

    Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al., 2003 as Paenisporosarcina macmurdoensis comb. nov

    Int. J. Syst. Evol. Microbiol.

    (2009)
  • S. Krishnamurthi et al.

    Re-examination of taxonomic position of Bacillus silvestris Rheims et al. 1999 and proposal to transfer it to a new genus Solibacillus gen. nov. as Solibacillus silvestris comb. nov

    Int. J. Syst. Evol. Microbiol.

    (2009)
  • B. Lányi

    Classical and rapid identification methods for medically important bacteria

    Methods Microbiol.

    (1987)
  • I. Lee et al.

    OrthoANI: an improved algorithm and software for calculating average nucleotide identity

    Int. J. Syst. Evol. Microbiol.

    (2016)
  • N.A. Logan et al.

    Genus I. Bacillus

  • N.A. Logan et al.

    Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria

    Int. J. Syst. Evol. Microbiol.

    (2009)
  • P.L. Manachini et al.

    Bacillus thermodenitrificans sp. nov., nom. rev

    Int. J. Syst. Evol. Microbiol.

    (2000)
  • J.P. Meier-Kolthoff et al.

    Genome sequence-based species delimitation with confidence intervals and improved distance functions

    BMC Bioinformatics

    (2013)
  • J.P. Meier-Kolthoff et al.

    Taxonomic use of DNA G + C content and DNA–DNA hybridization in the genomic age

    Int. J. Syst. Evol. Microbiol.

    (2014)

    • Cited by (5)

    ☆

    The GenBank accession numbers for the 16S rRNA gene sequence of strains “B. aminovorans” DSM 1314T and “B. aminovorans” DSM 4337 are LT174524 and LT174523. NCBI Bioproject accession numbers for the draft genome sequence of strains “B. aminovorans” strains DSM 1314T, DSM 4337, Domibacillus iocasae DSM 29979T and D. antri KCTC 33636T are LQWY00000000, LQWZ00000000, MAMP00000000 and MSDU00000000, respectively.

    View full text
    © 2017 Elsevier GmbH. All rights reserved.