Skip to main content

Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing bacteria isolated from soil of ginseng field


A novel bacterial strain DCY89T was isolated from soil sample of ginseng field and was characterized using a polyphasic approach. Cells were Gram-reaction-positive, rod-shaped, spore-forming and motile with flagella. The strain was aerobic, esculin and starch positive, catalase- and oxidase-negative, optimum growth temperature, and pH were 25–30 °C and 6.0–7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain DCY89T was shown to belong to the genus Paenibacillus and the closest phylogenetic relatives were Paenibacillus cellulosilyticus KACC 14175T (98.2%), Paenibacillus kobensis KACC 15273T (98.1%), Paenibacillus xylaniclasticus KCTC 13719T (96.9%), and Paenibacillus curdlanolyticus KCTC 3759T (96.64%). The DNA G+C content was 52.5 mol%, and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15:0, iso-C16:0, and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that DCY89T represented a novel species within the genus Paenibacillus, for which we propose the name Paenibacillus ginsengiterrae. The type strain is DCY89T (JCM 19887T = KCTC 33430T).

This is a preview of subscription content, access via your institution.

Fig. 1


  • Ash C, Priest FG, Collins MD (1993) 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 64:253–260

    Article  CAS  PubMed  Google Scholar 

  • Baik KS, Lim CH, Choe HN, Kim EM, Seong CN (2011) Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int J Syst Evol Microbiol 61:529–534

    Article  CAS  PubMed  Google Scholar 

  • Bauer AW, Kirby WM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496

    CAS  PubMed  Google Scholar 

  • Berge O, Guinebretière MH, Achouak W, Normand P, Heulin T (2002) Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 52:607–616

    CAS  PubMed  Google Scholar 

  • Cheong H, Park SY, Ryu CM, Kim JF, Park SH, Park CS (2005) Diversity of root-associated Paenibacillus spp. in winter crops from the southern part of Korea. J Microbiol Biotechnol 15:1286–1298

    CAS  Google Scholar 

  • Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354

    PubMed Central  CAS  PubMed  Google Scholar 

  • Cowan ST, Steel KJ (1974) Manual for the identification of medical bacteria. Cambridge University Press, Cambridge

    Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid hybridization in micro dilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bact 39:224–229

    Article  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Glaeser SP, Falsen E, Busse HJ, Kämpfer P (2013) Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 63:777–782

    Article  CAS  PubMed  Google Scholar 

  • Kim MK, Im WT, Ohta H, Lee M, Lee S-T (2005) Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43:152–157

    CAS  PubMed  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, Willey (ed) Nucleic Acid Techniques in Bacterial Systematics

  • Lim JM, Jeon CO, Lee JC, Xu LH, Jiang CL, Kim CJ (2006) Paenibacillus gansuensis sp. nov., isolated from desert soil of Gansu Province in China. Int J Syst Evol Microbiol 56:2131–2134

    Article  CAS  PubMed  Google Scholar 

  • Ludwig W, Schleifer KH, Whitman WB (2009) Family IV. Paenibacillaceae fam. nov. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey F, Schleifer KH, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 3, 2nd edn. Springer, New York, p 269

    Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Evol Microbiol 39:159–167

    CAS  Google Scholar 

  • Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Evol Microbiol 27:104–117

    CAS  Google Scholar 

  • Quan LH, Min JW, Yang DU, Kim YJ, Yang DC (2012) Enzymatic biotransformation of ginsenoside Rb1 to 20(S)-Rg3 by recombinant β-glucosidase from Microbacterium esteraromaticum. Appl Microbiol Biotechnol 94:377–384

    Article  CAS  PubMed  Google Scholar 

  • Rivas R, Mateos PF, Martínez-Molina E, Velázquez E (2005) Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 55:405–408

    Article  CAS  PubMed  Google Scholar 

  • Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E (2006) Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol 56:2777–2781

    Article  CAS  PubMed  Google Scholar 

  • Roux V, Raoult D (2004) Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. Int J Syst Evol Microbiol 54:1049–1054

    Article  CAS  PubMed  Google Scholar 

  • Saha P, Mondal AK, Mayilraj S, Krishnamurthi S, Bhattacharya A, Chakrabarti T (2005) Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India. Int J Syst Evol Microbiol 55:2577–2581

    Article  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

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark

  • Scheldeman P, Goossens K, Rodriguez-Diaz M, Pil A, Goris J, Herman L, De Vos P, Logan NA, Heyndrickx M (2004) Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk. Int J Syst Evol Microbiol 54:885–891

    Article  CAS  PubMed  Google Scholar 

  • Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    PubMed Central  CAS  PubMed  Google Scholar 

  • Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47:289–298

    Article  CAS  PubMed  Google Scholar 

  • Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. The Williams & Wilkins Co, Baltimore

    Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    PubMed Central  CAS  PubMed  Google Scholar 

  • Taibi G, Schiavo MR, Gueli MC, Rindina PC, Muratore R, Nicotra CM (2000) Rapid and simultaneous high–performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr Biomed Sci Appl 745:431–437

    Article  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Valverde A, Peix A, Rivas R, Velá-zquez E, Salazar S, Santa-Regina I, Rodríguez-Barrueco C, Igual JM (2008) Paenibacillus castaneae sp. nov., isolated from the phyllosphere of Castanea sativa Miller. Int J Syst Evol Microbiol 58:2560–2564

    Article  CAS  PubMed  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE et al (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bact 37:463–464

    Article  Google Scholar 

  • Weon HY, Kim BY, Joa JH, Son JA, Song MH, Kwon SW, Go SJ, Yoon SH (2008) Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 58:93–96

    Article  CAS  PubMed  Google Scholar 

  • Yao R, Wang R, Wang D, Su J, Zheng SX, Wang G (2014) Paenibacillus selenitireducens sp. nov., a selenite-reducing bacterium isolated from a selenium mineral soil. Int J Syst Evol Microbiol 64:805–811

    Article  CAS  PubMed  Google Scholar 

  • Zhou Y, Gao S, Wei DQ, Yang LL, Huang X, He J, Zhang YJ, Tang SK, Li WJ (2012) Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. Antonie van Leeuwenhoek 102:601–609

    Article  CAS  PubMed  Google Scholar 

Download references


This research was supported by Korea Institute of Planning & Evaluation for Technology in Food, Agriculture, Forestry & Fisheries (KIPET NO: 309019-03-3-SB010) and Next-Generation BioGreen 21 Program (SSAC, Grant#: PJ009529032014), Republic of Korea.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Yeon-Ju Kim or Deok-Chun Yang.

Additional information

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DCY89T is KF915799.

Communicated by Erko Stackebrandt.

Electronic supplementary material

Below is the link to the electronic supplementary material.


Two-dimensional TLC of the total polar lipids of strain P. ginsengiterrae DCY89T (A) and P. cellulosilyticus KACC 14175T (B), stained for total polar lipids with 5% ethanolic molybdophosphoric acid. Abbreviations: DPG, diphosphatidylglycerol; PE, phosphatidylethanolamine; PG, phosphatidylglycerol. (TIFF 18,421kb)

Transmission electron micrograph of P. ginsengiterrae DCY89T. Bar, 0.5μm (TIFF 3,270kb)

Spore-formation by P. ginsengiterrae DCY89T. (TIFF 2,258 kb)


The maximum-likelihood (ML) tree based on 16S rRNA gene sequence analysis showing phylogenetic relationships of strain DCY89T and members of the genus Paenibacillus. (PPTX 89kb)

Time-course TLC analysis of metabolite of ginsenoside Rb1 by P. ginsengiterrae DCY89T. C, control; S, saponin standards (TIFF 390kb)


HPLC profiles of metabolite of ginsenoside Rb1 converted by P. ginsengiterrae DCY89T. A, ginsenoside standards; B, ginsenoside Rb1 control and C, ginsenoside Rb1 metabolite. (TIFF 977kb)


Mass spectra of ginsenoside Rb1 after hydrolysis by P. ginsengiterrae DCY89T. (A) Mass spectrum of standard ginsenoside Rd; (B) Mass spectrum of bioconverted ginsenoside Rd. (TIFF 1,507kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Huq, M.A., Kim, YJ., Hoang, VA. et al. Paenibacillus ginsengiterrae sp. nov., a ginsenoside-hydrolyzing bacteria isolated from soil of ginseng field. Arch Microbiol 197, 389–396 (2015).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Paenibacillus ginsengiterrae
  • Ginseng soil
  • Taxonomy
  • Biotransformation