1887

Abstract

The conversion of major ginsenosides into minor ginsenosides attracts a lot of interest because of their biological and pharmaceutical activities. Therefore, for the conversion of ginsenosides, finding a novel competent glycoside hydrolase-producing bacterial strain is useful for future research studies and the mass production of minor ginsenosides. Wastewater samples were collected and screened for novel glycoside hydrolase bacterial strains using Reasoner's 2A+aesculin agar medium. As a result, a novel glycoside hydrolase positive bacterial strain (SB-02) was identified and subjected to a polyphasic taxonomic analysis. Based on genome analysis, strain SB-02 was found to be affiliated with the family and have less than 92.8 % sequence similarity to other members of the same family. Functional analysis indicated that SB-02 was able to hydrolyse the ginsenosides Rb1, Rc and Rd to F2 and C-K. Due to the conversion of ginsenosides, the strain’s genome was sequenced and the genes were annotated by the NCBI. The average amino acid identity and average nucleotide identity values between SB-02 and the available reference genomes were 65.7 and 65.9 %, respectively. The novel isolate contained MK-7 as the predominant menaquinone, the major polyamine putrescine, and iso-C, iso-C G and iso-C 3-OH as major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Thus, based on the data presented here, strain SB-02 represents a novel species within a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is SB-02 (=KACC 21266=LMG 31707). The genome annotation of SB-02 shows many glycoside hydrolase genes, which may be responsible for the efficient production of many kinds of minor ginsenosides and will be very helpful for future research (target gene cloning) and mass production of either F2 or C-K.

Funding
This study was supported by the:
  • This work was supported by a research grant from Hankyong National University in the year of 2019.
    • Principle Award Recipient: Muhammadzubair Siddiqi
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004793
2021-05-11
2022-01-24
Loading full text...

Full text loading...

References

  1. Cho I-H. Effects of Panax ginseng in neurodegenerative diseases. J Ginseng Res 2012; 36:342–353 [View Article]
    [Google Scholar]
  2. Attele AS, Wu JA, Yuan CS. Ginseng pharmacology: multiple constituents and multiple actions. Biochem Pharmacol 1999; 58:1685–1693 [View Article][PubMed]
    [Google Scholar]
  3. Wee JJ, MP K, Chung AS. Biological activities of ginseng and its application to human health. In Benzie IFF, Wachtel-Galor S. (editors) Herbal Medicine: Biomolecular and Clinical Aspects, 2nd edition. Boca Raton, FL: CRC Press/Taylor and Francis; 2011 p Chapter 8
    [Google Scholar]
  4. Yuan C-S, Wu JA, Osinski J. Ginsenoside variability in American ginseng samples. Am J Clin Nutr 2002; 75:600–601 [View Article][PubMed]
    [Google Scholar]
  5. Park HJ, Kim DH, Park SJ, Kim JM, Ryu JH. Ginseng in traditional herbal prescriptions. J Ginseng Res 2012; 36:225–241 [View Article][PubMed]
    [Google Scholar]
  6. Shin B-K, Kwon SW, Park JH. Chemical diversity of ginseng saponins from Panax ginseng. J Ginseng Res 2015; 39:287–298 [View Article][PubMed]
    [Google Scholar]
  7. Christensen LP. Ginsenosides chemistry, biosynthesis, analysis, and potential health effects. Adv Food Nutr Res 2009; 55:1–99 [View Article][PubMed]
    [Google Scholar]
  8. Shin JY, Lee JM, Shin HS, Park SY, Yang JE et al. Anti-Cancer effect of ginsenoside F2 against glioblastoma multiforme in xenograft model in SD rats. J Ginseng Res 2012; 36:86–92 [View Article][PubMed]
    [Google Scholar]
  9. Yuan H-D, Kim JT, Kim SH, Chung SH. Ginseng and diabetes: the evidences from in vitro, animal and human studies. J Ginseng Res 2012; 36:27–39 [View Article][PubMed]
    [Google Scholar]
  10. Siddiqi MZ, Siddiqi MH, Kim Y-J, Jin Y, Huq MA et al. Effect of fermented red ginseng extract enriched in ginsenoside Rg3 on the differentiation and mineralization of preosteoblastic MC3T3-E1 cells. J Med Food 2015; 18:542–548 [View Article][PubMed]
    [Google Scholar]
  11. Baatar D, Siddiqi MZ, Im WT, Khaliq N, Hwang SG. Anti-inflammatory effect of ginsenoside Rh 2 -mix on lipopolysaccharide-stimulated RAW 264.7 Murine macrophage cells. J Med Food 2018; 21:951–960 [View Article]
    [Google Scholar]
  12. Siddiqi MZ, Im W-T. Pseudobacter ginsenosidimutans gen. nov., sp. nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2016; 66:3449–3455 [View Article][PubMed]
    [Google Scholar]
  13. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im W-T. Compostibacter hankyongensis gen. nov.,  sp. nov., isolated from compost. Int J Syst Evol Microbiol 2016a; 66:3681–3687 [View Article][PubMed]
    [Google Scholar]
  14. SR K, Choi KJ, Suzuki K, Suzuki Y. Enzymatic preparation of ginsenosides Rg2, Rh1, and F1. Chem Pharm Bull 2003; 51:404–408
    [Google Scholar]
  15. Siddiqi MZ, Srinivasan S, Park HY, Im W-T. Exploration and characterization of novel glycoside hydrolases from the whole genome of Lactobacillus ginsenosidimutans and enriched production of minor ginsenoside Rg3(S) by a recombinant enzymatic processs. Biomolecules 2020; 10:288 12 02 2020 [View Article][PubMed]
    [Google Scholar]
  16. Siddiqi MZ, Hashmi MS, Oh J-M, Chun S, Im W-T. Identification of novel glycoside hydrolases via whole genome sequencing of Niabella ginsenosidivorans for production of various minor ginsenosides. 3 Biotech 2019; 9:258 [View Article][PubMed]
    [Google Scholar]
  17. Siddiqi MZ, Muhammad Shafi S, Choi KD, Im W-T. Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2016b; 66:4039–4045 [View Article][PubMed]
    [Google Scholar]
  18. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  19. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  20. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  21. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  22. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  24. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  26. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27:4636–4641 [View Article][PubMed]
    [Google Scholar]
  27. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
    [Google Scholar]
  28. Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278 [View Article][PubMed]
    [Google Scholar]
  29. Pagani I, Liolios K, Jansson J, Chen I-MA, Smirnova T et al. The genomes online database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012; 40:D571–D579 [View Article][PubMed]
    [Google Scholar]
  30. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
    [Google Scholar]
  31. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  32. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article][PubMed]
    [Google Scholar]
  33. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–655
    [Google Scholar]
  35. Nishijima M, Araki-Sakai M, Sano H. Identification of isoprenoid quinones by frit-FAB liquid chromatography–mass spectrometry for the chemotaxonomy of microorganisms. J Microbiol Methods 1997; 28:113–122 [View Article]
    [Google Scholar]
  36. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990 p 204
    [Google Scholar]
  37. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  38. Schenkel E, Berlaimont V, Dubois J, Helson-Cambier M, Hanocq M. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr B Biomed Appl 1995; 668:189–197 [View Article][PubMed]
    [Google Scholar]
  39. Liu M-J, Jin C-Z, Asem MD, Ju Y-J, Park D-J et al. Aurantisolimonas haloimpatiens gen. nov., sp. nov., a bacterium isolated from soil. Int J Syst Evol Microbiol 2018; 68:1552–1559 [View Article][PubMed]
    [Google Scholar]
  40. Zhang NN, Qu JH, Yuan HL, Sun YM, Yang JS. Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. Int J Syst Evol Microbiol 2010; 60:1609–1612 [View Article][PubMed]
    [Google Scholar]
  41. Shiratori H, Tagami Y, Morishita T, Kamihara Y, Beppu T et al. Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. Int J Syst Evol Microbiol 2009; 59:1137–1142 [View Article][PubMed]
    [Google Scholar]
  42. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  43. Xie C-H, Yokota A. Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil. Int J Syst Evol Microbiol 2006; 56:1117–1121 [View Article][PubMed]
    [Google Scholar]
  44. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 1981; 31:285–293 [View Article]
    [Google Scholar]
  45. Kämpfer P, Young C-C, Sridhar KR, Arun AB, Lai WA et al. Transfer of [Flexibacter] sancti, [Flexibacter] filiformis, [Flexibacter] japonensis and [Cytophaga] arvensicola to the genus Chitinophaga and description of Chitinophaga skermanii sp. nov. Int J Syst Evol Microbiol 2006; 56:2223–2228 [View Article][PubMed]
    [Google Scholar]
  46. Lee D-H, Cha C-J. Flavihumibacter sediminis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2016; 66:4310–4314 [View Article][PubMed]
    [Google Scholar]
  47. Gao J-L, Sun P, Wang X-M, Qiu T-L, Lv F-Y et al. Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:2730–2734 [View Article][PubMed]
    [Google Scholar]
  48. Han S-I, Lee Y-R, Kim J-O, Whang K-S. Terrimonas rhizosphaerae sp. nov., isolated from ginseng rhizosphere soil. Int J Syst Evol Microbiol 2017; 67:391–395 [View Article][PubMed]
    [Google Scholar]
  49. Jin D, Kong X, Wang J, Sun J, Yu X et al. Chitinophaga caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:2209–2213 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004793
Loading
/content/journal/ijsem/10.1099/ijsem.0.004793
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error