Skip to main content
SpringerLink
Log in

Complete Genome of Vibrio neocaledonicus CGJ02-2, An active Compounds Producing Bacterium Isolated from South China Sea

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Strain CGJ02-2 was isolated from the coral reefs in South China sea and deposited in South China Sea Institute of Oceanology, Chinese Academy of Sciences. Active compounds including indole, ρ-hydroxybenzaldehyde were isolated from this strain. To explore the biosynthetic way of these compounds and search gene clusters, the complete genome of this strain was sequenced by Single Molecule, Real-Time (SMRT) technology. It was de novo assembled to two circular chromosomes of 3,400,283 bp with GC% 44.77 and 1,845,572 bp with GC% 44.59 respectively and classified as Vibrio alginolyticus. In silico phenotype features of Vibrio alginolyticus CGJ02-2 were also analyzed. The biosynthetic pathway of ρ-hydroxybenzaldehyde and indole in this strain were postulated. Gene clusters of four secondary metabolites including bacteriocin, ectoine, siderophore, arylpolyene were identified. This study provides helpful information for further utilizing Vibrio alginolyticus CGJ02-2 as a source of valuable bioactive compounds.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Tatusov RL, Fedorova ND, Jackson JD et al (2011) The neuroprotective effects of an extract of Gastrodia elata. J Ethnopharmacol 138:1–125

    Article  CAS  Google Scholar 

  2. Eddouks M, Bidi A, Bouhali BEL et al (2014) Insulin resistance as a target of some plant-derived phytocompounds. Stud Nat Prod Chem 43:351–373

    Article  CAS  Google Scholar 

  3. Oh SH, Ryu B, Ngo DH et al (2017) 4-hydroxybenzaldehy-de-chitoo-ligomers suppresses H2O2-induced oxidative damage in microglia BV-2 cells. Carbohydr Res 440–441:32–37

    Article  CAS  Google Scholar 

  4. Ha JH, Lee DU, Lee JT et al (2000) 4-hydroxybenzaldehyde from Gastrodia elata B1. Is active in the antioxidation and GABAergic neuromodulation of the rat brain. J Ethnopharmacol 73:329–333

    Article  CAS  Google Scholar 

  5. Ku MY, Li C, Yang Z et al (2011) New progress on synthesis of ρ-hydroxybenzaldehyde. Chem. Reagents 33:1087–1094+1107

  6. Lee JH (2010) Indole as an intercellular signal in microbial communities. FEMS Microbiol Rev 34:426–444

    Article  CAS  Google Scholar 

  7. ShenTu YD, ShenTU Y, Jin YQ et al (2005) A simple synthetic method of indole. ZJ Chem Ind 9:24–25

    Google Scholar 

  8. Gómez CI, Zhao JP, Tan L et al (2019) Bioactive compounds isolated from marine bacterium Vibrio neocaledonicus and their enzyme inhibitory activities. Mar Drugs 17:1–19

    Google Scholar 

  9. Tan L, Yisha B, Sun XR et al (2018) Natural indole, its preparation method and application for preparing drugs for treating Alzheimer's disease or diabetes, Jul 20, CN 108299274

  10. Lim HJ, Lee EH, Yoon Y et al (2016) Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 120:379–387

    Article  CAS  Google Scholar 

  11. Ardui S, Ameur A, Vermeesch JR, Hestand MS (2018) Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–2168

    Article  CAS  Google Scholar 

  12. Reiner J, Pisani L, Qiao W et al (2018) Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion. NPJ Genom Med 3:1–5

    Article  CAS  Google Scholar 

  13. Parks DH, Chuvochina M, Waite DW et al (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004

    Article  CAS  Google Scholar 

  14. Emms DM, Kelly S (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:1–14

    Article  CAS  Google Scholar 

  15. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:0955–964

    Article  CAS  Google Scholar 

  16. Lagesen K, Hallin PF, Rødland E et al (2007) RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 35:3100–3108

    Article  CAS  Google Scholar 

  17. Gardner PP, Daub J, Tate JG et al (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37:D136–D140

    Article  CAS  Google Scholar 

  18. Hsiao W, Wan I, Jones SJ, Brinkman FS (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19:418–420

    Article  Google Scholar 

  19. Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to indentify clustered regularly interspaced short palindromic repeat. Nucleic Acids Res 35:52–57

    Article  Google Scholar 

  20. Ashburner M, Ball CA, Blake JA et al (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  Google Scholar 

  21. Kanehisa M, Goto S, Hattori M et al (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357

    Article  CAS  Google Scholar 

  22. Tatusov RL, Fedorova ND, Jackson JD et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:1–14

    Article  Google Scholar 

  23. Li W, Jaroszewski L, Godzik A (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18:77–82

    Article  CAS  Google Scholar 

  24. Saier MHJ, Yen MR, Noto K et al (2009) The transporter classification database. Nucleic Acids Res 37:D274–D278

    Article  CAS  Google Scholar 

  25. Amos B, Rolf A (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45–48

    Article  Google Scholar 

  26. Amaral GRS, Dias GM, Wellington-Oguri M et al (2014) Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 64:357–365

    Article  CAS  Google Scholar 

  27. Aziz RK, Bartels D, Best AA et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:1–15

    Article  CAS  Google Scholar 

  28. Alvarado IE, Lomascolo A, Navarro D et al (2002) Evidence of a new biotransformation pathway of ρ-coumaric acid into ρ-hydroxybenzaldehyde in pycnoporus cinnebarius. Appl Microbiol Biotechnol 57:725–730

    Google Scholar 

  29. Jensen KAJR, Evans KMC, Kirk TK, Hammel KE (1994) Biosynthetic pathway for veratryl alcohol in the ligninolytic fungus Phanerochaete chrysosporium. Appl Environ Microbiol 60:709–714

    Article  CAS  Google Scholar 

  30. Walton NJ, Narbad A, Faulds CB et al (2000) Novel approaches to the biosynthesis of vanillin. Curr Opin Biotechnol 11:490–496

    Article  CAS  Google Scholar 

  31. Schöner TA, Gassel S, Osawa A et al (2016) Aryl polyenes, a highly abundant class of bacterial natural products, are functionally related to antioxidative carotenoids. Chem BioChem 17:247–253

    Google Scholar 

  32. Cotter PD, Ross RP, Hill C (2012) Bacteriocins: a viable alternative to antibiotics? Nat Rev Microbiol 11:95–105

    Article  CAS  Google Scholar 

  33. Silva Célia CG, Silva SPM, Ribeiro SC (2018) Application of bacteriocins and protective cultures in dairy food preservation. Front Microbiol 9:1–18

    Article  Google Scholar 

  34. Kobus N, Widderich A, Hoeppner E et al (2015) Overproduction, crystallization and X-Ray diffraction data analysis of ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis. Acta Crystallogr F 71:1027–1032

    Article  CAS  Google Scholar 

  35. Wyckoff EE, Allred BE, Raymond KN (2015) Catechol siderophore transport by vibrio cholerae. J Bacteriol 197:2840–2849

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was funded by Hainan Provincial Key Research and Development Program (ZDYF2019167)

Author information

Authors and Affiliations

  1. Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, Hainan, China

    Lin Tan, Isabel Gómez-Betancur, Suxia Guo, Yu Ge & Nan Wang

  2. Programa de Ofidismo/Escorpionismo, Facultad de Ciencias Farmacéuticas Y Alimentarias, Universidad de Antioquia, 1226, Medellín, Colombia

    Isabel Gómez-Betancur

  3. School of Pharmacy, National Center for Natural Products Research, Thad Cochran Research Center, University of Mississippi, University, MS, 38677, USA

    Jianping Zhao

  4. Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China

    Chang Chen

Authors
  1. Lin Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Isabel Gómez-Betancur
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Suxia Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yu Ge
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jianping Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Nan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Lin Tan or Chang Chen.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Research Involving Human and Animal Participants

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

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 469 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tan, L., Gómez-Betancur, I., Guo, S. et al. Complete Genome of Vibrio neocaledonicus CGJ02-2, An active Compounds Producing Bacterium Isolated from South China Sea. Curr Microbiol 77, 2665–2673 (2020). https://doi.org/10.1007/s00284-020-02047-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-020-02047-7

Search

Navigation