Browse > Article
http://dx.doi.org/10.4014/jmb.2208.08043

Characterization of Pseudomonas sp. NIBR-H-19, an Antimicrobial Secondary Metabolite Producer Isolated from the Gut of Korean Native Sea Roach, Ligia exotica  

Sungmin Hwang (Clean Energy Research Center, Korea Institute of Science and Technology (KIST))
Jun Hyeok Yang (Laboratory of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime and Ocean University)
Ho Seok Sim (Laboratory of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime and Ocean University)
Sung Ho Choi (National Institute of Biological Resources, Environmental Research Complex)
Byounghee Lee (National Institute of Biological Resources, Environmental Research Complex)
Woo Young Bang (National Institute of Biological Resources, Environmental Research Complex)
Ki Hwan Moon (Laboratory of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime and Ocean University)
Publication Information
Journal of Microbiology and Biotechnology / v.32, no.11, 2022 , pp. 1416-1426 More about this Journal
Abstract
The need to discover new types of antimicrobial agents has grown since the emergence of antibiotic-resistant pathogens that threaten human health. The world's oceans, comprising complex niches of biodiversity, are a promising environment from which to extract new antibiotics-like compounds. In this study, we newly isolated Pseudomonas sp. NIBR-H-19 from the gut of the sea roach Ligia exotica and present both phenotypes and genomic information consisting of 6,184,379 bp in a single chromosome possessing a total of 5,644 protein-coding genes. Genomic analysis of the isolated species revealed that numerous genes involved in antimicrobial secondary metabolites are predicted throughout the whole genome. Moreover, our analysis showed that among twenty-five pathogenic bacteria, the growth of three pathogens, including Staphylococcus aureus, Streptococcus hominis and Rhodococcus equi, was significantly inhibited by the culture of Pseudomonas sp. NIBR-H-19. The characterization of marine microorganisms with biochemical assays and genomics tools will help uncover the biosynthesis and action mechanism of antimicrobial metabolites for development as antagonistic probiotics against fish pathogens in an aquatic culture system.
Keywords
Antibiotics; Ligia exotica; secondary metabolite; symbiotic bacterium; Pseudomonas sp.;
Citations & Related Records
Times Cited By KSCI : 11  (Citation Analysis)
연도 인용수 순위
1 Afzal S, Yadav AK, Poonia AK, Choure K, Yadav AN, Pandey A. 2022. Antimicrobial therapeutics isolated from algal source: retrospect and prospect. Biologua 20: 1-15. 
2 Parameswari RP, Lakshmi T. 2022. Microalgae as a potential therapeutic drug candidate for neurodegenerative diseases. J. Biotechnol. 358: 128-139.    DOI
3 Wu MJ, Xu B, Guo YW. 2022. Unusual secondary metabolites from the mangrove ecosystems: Structures, bioactivities, chemical, and bio-syntheses. Mar. Drugs 20: 535. 
4 Perry EK, Meirelles LA. 2022. From the soil to the clinic: the impact of microbial secondary metabolites on antibiotic tolerance and resistance. Nat. Rev. Microbiol. 20: 129-142.   DOI
5 Ventola CL. 2015. The antibiotic resistance crisis: part 1: causes and threats. Pharm. Ther. 40: 277. 
6 Munita JM, Arias CA. 2016. Mechanisms of antibiotic resistance. Microbiology spectrum. 4. doi.org/10.1128/microbiolspec.VMBF-0016-2015.    DOI
7 Chevrette MG, Carlson CM, Ortega HE, Thomas C, Ananiev GE, Barns KJ, et al. 2019. The antimicrobial potential of Streptomyces from insect microbiomes. Nat. Commun. 10: 516. 
8 Jun JY, Jung MJ, Jeong IH, Yamazaki K, Kawai Y, Kim BM. 2018. Antimicrobial and antibiofilm activities of sulfated polysaccharides from marine algae against dental plaque bacteria. Mar. Drugs. 16: 301. 
9 Rooks MG, Garrett WS. 2016. Gut microbiota, metabolites and host immunity. Nat. Rev. Immunol. 16: 341-352.    DOI
10 Braig HR, Perotti MA. 2009. Carcases and mites. Exp. Appl. Acarol. 49: 45-84.    DOI
11 Garcia-Hernandez J, Hurtado LA, Leyva-Garcia G, Guido-Moreno A, Aguilera-Marquez D, Mazzei V, et al. 2015. Isopods of the genus Ligia as potential biomonitors of trace metals from the gulf of California and pacific coast of the Baja California peninsula. Ecotoxicol. Environ. Safety 112: 177-185.    DOI
12 Ghosh J, Lun CM, Majeske AJ, Sacchi S, Schrankel CS, Smith LC. 2011. Invertebrate immune diversity. Dev. Comp. Immunol. 35: 959-974.    DOI
13 Padfield D, Castledine M, Buckling A. 2020. Temperature-dependent changes to host-parasite interactions alter the thermal performance of a bacterial host. ISME J. 14: 389-398.    DOI
14 Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.    DOI
15 Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.    DOI
16 Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.    DOI
17 Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.    DOI
18 Fleming A. 1980. Classics in infectious diseases: on the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae by Alexander Fleming, Reprinted from the British Journal of Experimental Pathology 10:226-236, 1929. Rev. Infect. Dis. 2: 129-139.    DOI
19 Vachee A, Mossel DA, Leclerc H. 1997. Antimicrobial activity among Pseudomonas and related strains of mineral water origin. J. Appl. Microbiol. 83: 652-658.    DOI
20 El-Sheshtawy H, Doheim M. 2014. Selection of Pseudomonas aeruginosa for biosurfactant production and studies of its antimicrobial activity. Egypt. J. Petroleum 23: 1-6.    DOI
21 Terreni M, Taccani M, Pregnolato M. 2021. New antibiotics for multidrug-fesistant bacterial strains: latest research developments and future perspectives. Molecules 26: 2671. 
22 Enright MC, Robinson DA, Randle G, Feil EJ, Grundmann H, Spratt BG. 2002. The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc. Natl. Acad. Sci. USA 99: 7687-7692.    DOI
23 Thompson T. 2022. The staggering death toll of drug-resistant bacteria. Nature doi: 10.1038/d41586-022-00228-x. Online ahead of print.    DOI
24 Davies O, Bennett S. 2017. WHO publishes list of bacteria for which new antibiotics are urgently needed. WHO Newsletters. 
25 Cook MA, Wright GD. 2022. The past, present, and future of antibiotics. Sci. Transl. Med. 14: eabo7793. 
26 Thumar JT, Dhulia K, Singh SP. 2010. Isolation and partial purification of an antimicrobial agent from halotolerant alkaliphilic Streptomyces aburaviensis strain Kut-8. World J. Microbiol. Biotechnol. 26: 2081-2087.   DOI
27 Bhalodi AA, van Engelen TSR, Virk HS, Wiersinga WJ. 2019. Impact of antimicrobial therapy on the gut microbiome. J. Antimicrob. Chemother. 74: i6-i15.    DOI
28 Solomon SL, Oliver KB. 2014. Antibiotic resistance threats in the United States: stepping back from the brink. Am. Family Phys. 89: 938-941. 
29 Shrivastava SR, Shrivastava PS, Ramasamy J. 2018. World health organization releases global priority list of antibiotic-resistant bacteria to guide research, discovery, and development of new antibiotics. J. Med. Soc. 32: 76-77.    DOI
30 Furfaro LL, Payne MS, Chang BJ. 2018. Bacteriophage therapy: clinical trials and regulatory hurdles. Front. Cell. Infect. Microbiol. 8: 376. 
31 Roux D, Pier GB, Skurnik D. 2012. Magic bullets for the 21st century: the reemergence of immunotherapy for multi- and pan-resistant microbes. J. Antimicrob. Chemother. 67: 2785-2787.    DOI
32 Piddock LJV. 2015. Teixobactin, the first of a new class of antibiotics discovered by iChip technology? J. Antimicrob. Chemother. 70: 2679-2680.    DOI
33 Li LG, Yin X, Zhang T. 2018. Tracking antibiotic resistance gene pollution from different sources using machine-learning classification. Microbiome 6: 93. 
34 Beesoo R, Bhagooli R, Neergheen-Bhujun VS, Li WW, Kagansky A, Bahorun T. 2017. Antibacterial and antibiotic potentiating activities of tropical marine sponge extracts. Comp. Biochem. Physiol. C Toxicol. Pharmacol. 196: 81-90.    DOI
35 Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. 2018. KBase: the united states department of energy systems biology knowledgebase. Nat. Biotechnol. 36: 566-569.    DOI
36 Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35: 3100-3108.    DOI
37 Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47: W81-W87.    DOI
38 Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38: 3022-3027.    DOI
39 Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CKwnfm, et al. 2003. Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. Int. J. Syst. Evol. Microbiol. 53: 21-27.    DOI
40 Peix A, Rivas R, Mateos PF, Martinez-Molina E, Rodriguez-Barrueco C, Velazquez E. 2003. Pseudomonas rhizosphaerae sp. nov., a novel species that actively solubilizes phosphate in vitro. Int. J. Syst. Evol. Microbiol. 53: 2067-2072.    DOI
41 Ramette A, Frapolli M, Fischer-Le Saux M, Gruffaz C, Meyer JM, Defago G, et al. 2011. Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Syst. Appl. Microbiol. 34: 180-188.    DOI
42 Singh H, Du J, Singh P, Yi TH. 2018. Extracellular synthesis of silver nanoparticles by Pseudomonas sp. THG-LS1.4 and their antimicrobial application. J. Pharm. Anal. 8: 258-264.    DOI
43 Piewngam P, Zheng Y, Nguyen TH, Dickey SW, Joo HS, Villaruz AE, et al. 2018. Pathogen elimination by probiotic Bacillus via signalling interference. Nature 562: 532-537.    DOI
44 Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW. 2011. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol. Rev. 35: 652-680.    DOI
45 Liu Y, Rao Q, Blom J, Lin Q, Luo T. 2020. Pseudomonas piscis sp. nov., isolated from the profound head ulcers of farmed Murray cod (Maccullochella peelii peelii). Int. J. Syst. Evol. Microbiol. 70: 2732-2739.    DOI
46 Karbalaei-Heidari HR, Budisa N. 2020. Combating antimicrobial resistance with new-to-nature lanthipeptides created by genetic code expansion. Front. Microbiol. 11: 590522. 
47 Stincone P, Fonseca Veras F, Micalizzi G, Donnarumma D, Vitale Celano G, Petras D, et al. 2022. Listeria monocytogenes exposed to antimicrobial peptides displays differential regulation of lipids and proteins associated to stress response. Cell Mol. Life Sci. 79: 263. 
48 Wu CY, Chen CL, Lee YH, Cheng YC, Wu YC, Shu HY, et al. 2007. Nonribosomal synthesis of fengycin on an enzyme complex formed by fengycin synthetases. J. Biol. Chem. 282: 5608-5616.    DOI
49 Dassama LM, Kenney GE, Rosenzweig AC. 2017. Methanobactins: from genome to function. Metallomics 9: 7-20.    DOI
50 Guzman J, Vilcinskas A. 2021. Genome analysis suggests the bacterial family Acetobacteraceae is a source of undiscovered specialized metabolites. Antonie Van Leeuwenhoek 115: 41-58.    DOI
51 Jurado-Martin I, Sainz-Mejias M. 2021. Pseudomonas aeruginosa: An audacious pathogen with an adaptable arsenal of virulence factors. Int. J. Mol. Sci. 22: 3128. 
52 Decoin V, Barbey C, Bergeau D, Latour X, Feuilloley MG, Orange N, et al. 2014. A type VI secretion system is involved in Pseudomonas fluorescens bacterial competition. PLoS One 9: e89411. 
53 Khaligh SF, Asoodeh A. 2022. Recent advances in the bio-application of microalgae-derived biochemical metabolites and development trends of photobioreactor-based culture systems. 3 Biotech 12: 260. 
54 Keita K, Darkoh C. 2022. Secondary plant metabolites as potent drug candidates against antimicrobial-resistant pathogens. SN Appl. Sci. 4: 209. 
55 Ndlovu T, Rautenbach M, Vosloo JA, Khan S, Khan W. 2017. Characterisation and antimicrobial activity of biosurfactant extracts produced by Bacillus amyloliquefaciens and Pseudomonas aeruginosa isolated from a wastewater treatment plant. AMB Express 7: 108.