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Chitinophaga chungangae sp. nov., isolated from a Korean grape garden and its potential to biosynthesize ginsenoside Rg2

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Abstract

A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain MAH-28 T hydrolyzed aesculin, casein and DNA. Flexirubin-type pigments are present. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MAH-28 T formed a cluster within the genus Chitinophaga and the most close relatives were Chitinophaga alhagiae T22T (98.9% 16S rRNA gene sequence similarity), Chitinophaga humicola Ktm-2 T (98.8%), Chitinophaga barathri YLT18T (98.3%) and Chitinophaga lutea ZY74T (97.4%). The novel strain MAH-28 T has a draft genome size of 6,043,180 bp (14 contigs), annotated with 4,863 protein-coding genes, 53 tRNA and 6 rRNA genes. The ANI and dDDH values between strain MAH-28 T and the closely related type strains were in the range of 76.0–83.4% and 20.3–26.7%, respectively. The novel strain MAH-28 T was able to synthesize ginsenoside Rg2 from major ginsenoside Re. The genome annotation revealed 152 carbohydrate genes which may involve with the synthesis of ginsenoside Rg2. The respiratory quinone of strain MAH-28 T was MK-7 and the dominant cellular fatty acids were C15:0 iso, C16:1 ω5c and C17:0 iso 3-OH. The DNA G + C content of strain MAH-28 T was 53.3 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic studies, strain MAH-28 T represents a new member of genus Chitinophaga for which the name Chitinophaga chungangae sp. nov. is proposed with type strain MAH-28 T (= KACC 19968 T = CGMCC 1.16605 T).

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References

  • Akter S, Huq MA (2018) Biological synthesis of ginsenoside Rd using Paenibacillus horti sp. nov. isolated from vegetable garden. Curr Microbiol 75:1566–1573

    Article  CAS  PubMed  Google Scholar 

  • Akter S, Huq MA (2020) Biologically rapid synthesis of silver nanoparticles by Sphingobium sp. MAH-11 T and their antibacterial activity and mechanisms investigation against drug-resistant pathogenic microbes. Artif Cells Nanomed Biotechnol 48:672–682

    Article  CAS  PubMed  Google Scholar 

  • Akter S, Lee SY, Siddiqi MZ, Balusamy SR, Ashrafudoulla M, Rupa EJ, Huq MA (2020) Ecofriendly synthesis of silver nanoparticles by Terrabacter humi sp. nov., and their antibacterial application against antibiotic-resistant pathogens. Int J Mol Sci 21:9746

    Article  CAS  PubMed Central  Google Scholar 

  • Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD (2015) RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365

    Article  PubMed  PubMed Central  Google Scholar 

  • Chaudhary DK, Kim J (2018) Chitinophaga humicola sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 68:751–757

    Article  CAS  PubMed  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  PubMed  Google Scholar 

  • Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P (ed) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 21–33

    Google Scholar 

  • Farh MA, Kim YJ, Van AH, Sukweenadhi J, Singh P, Huq MA, Yang DC (2015) Burkholderia ginsengiterrae sp. nov. and Burkholderia panaciterrae sp. nov., antagonistic bacteria against root rot pathogen Cylindrocarpon destructans, isolated from ginseng soil. Arch Microbiol 197:439–447

    Article  CAS  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA gene. Appl Environ Microbiol 74:2461–2470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geraldi A (2020) Advances in the production of minor ginsenosides using microorganisms and their enzymes. BIO Integration 1:15–24

    Article  Google Scholar 

  • Guo L, Tuo L, Habden X, Zhang Y, Liu J (2015) Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 65:206–213

    Article  CAS  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Huq MA (2017) Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden. Arch Microbiol. https://doi.org/10.1007/s00203-017-1469-8

    Article  PubMed  Google Scholar 

  • Huq MA (2018) Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden. Arch Microbiol 200:343–348

    Article  CAS  PubMed  Google Scholar 

  • Huq MA, Siraj FM, Kim YJ, Yang DC (2016) Enzymatic transformation of ginseng leaf saponin by recombinant β-glucosidase (bgp1) and its efficacy in an adipocyte cell line. Biotechnol Appl Biochem 63:532–538

    Article  CAS  PubMed  Google Scholar 

  • Kämpfer P, Lodders N, Falsen E (2011) Hydrotalea flava gen. n ov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 61:518–523

    Article  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60

    Article  PubMed  PubMed Central  Google Scholar 

  • Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214

    Article  CAS  PubMed  Google Scholar 

  • Reichenbach H (1992) The order Cytophagales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, vol 4, 2nd edn. Springer, New York, pp 3631–3675

  • Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sangkhobol V, Skerman VBD (1981) Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Bacteriol 31:285–293

    Article  Google Scholar 

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

  • Shi W, Sun Q, Fan G et al (2021) gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 49(D1):D694–D705

    Article  CAS  PubMed  Google Scholar 

  • Siddiqi MZ, Siddiqi MH, Kim YJ, Jin Y, Huq MA, Yang DC (2015) Effect of fermented red ginseng extract enriched in ginsenoside Rg3 on the differentiation and mineralization of preosteoblastic MC3T3-E1 cells. J Med Food 18:542–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Siraj FM, Natarajan S, Huq MA, Kim YJ, Yang DC (2015) Structural investigation of ginsenoside Rf with PPARγ major transcriptional factor of adipogenesis and its impact on adipocyte. J Gins Res 39:141–147

    Article  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Liao S, Tan Y, Wang G, Dan W, Zheng S (2015) Chitinophaga barathri sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 65:4233–4238

    Article  CAS  PubMed  Google Scholar 

  • Zong Y, Wu M, Liu X, Jin Y, Wang G, Li M (2019) Chitinophaga lutea sp. nov., isolated from arsenic-contaminated soil. Int J Syst Evol Microbiol 69:2114–2119

    Article  CAS  PubMed  Google Scholar 

  • Zou Y, Zhang X, Song H, Li Y, Cheng Q (2019) Chitinophaga alhagiae sp. Nov., isolated from rhizosphere soil of Alhagi sparsifolia. Int J Syst Evol Microbiol 69:1179–1184

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

I would like to give special thanks to CGM 10K project for analyzing the draft genome sequence of strain MAH-28T (GCM60012297).

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Authors and Affiliations

  1. Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea

    Md. Amdadul Huq

  2. Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea

    Shahina Akter

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  1. Md. Amdadul Huq
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  2. Shahina Akter
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Correspondence to Md. Amdadul Huq or Shahina Akter.

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Communicated by Erko Stackebrandt.

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The NCBI GenBank accession numbers for the 16S rRNA gene sequence and draft genome sequence of strains MAH-28 T are MK204991 and JAGHKP000000000, respectively.

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Huq, M.A., Akter, S. Chitinophaga chungangae sp. nov., isolated from a Korean grape garden and its potential to biosynthesize ginsenoside Rg2. Arch Microbiol 203, 5483–5489 (2021). https://doi.org/10.1007/s00203-021-02533-x

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