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WGS-based characterization of the potentially beneficial Enterococcus faecium EFD from a beehive

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Abstract

Nowadays, due to their potential application as probiotics for humans or animals, many beneficial lactic acid bacteria have been isolated from different natural environments. These include members of the genus Enterococcus - quite specific due to their ambiguous nature, varying from pathogens to probiotics. In our work we present a whole-genome sequencing (WGS)-based approach for assessing the potential of bacteriocin-producing Enterococcus isolates from beehives to serve as natural preserving agents against bacterial infections associated with honeybees. Potential Enterococcus spp. isolates from pollen granules were tested with the well diffusion assay for bacteriocin activity against Paenibacillus larvae, the causative agent of the American foulbrood disease (AFB). Two of them gave positive results and were determined at species level by 16S rRNA genes sequencing. They were then subjected to WGS using the Illumina HiSeq platform. The resulting raw data reads were processed and further analyzed by using only freely available web-based tools (the Shovill pipeline, QUAST, BAGEL4, ResFinder, VirulenceFinder and PlasmidFinder). The analysis revealed that both of them represent clonally identical isolates of the same strain. This specific strain was named Enterococcus faecium EFD, and was genotyped by the MLST-2.0 Server. Five bacteriocin genes were found in the assembled genome, providing a possible explanation for the antimicrobial properties of the isolate. The protein nature of the inhibitory agent/s was confirmed by treatment with proteinase K. No resistance determinants for clinically important antibiotics and functional virulence factor genes were detected. The bioinformatic analyses of the draft genome sequence suggest that E. faecium EFD is not pathogenic.The observation that E. faecium EFD was present within more than one of the beehives in the apiary proposes the idea that E. faecium EFD is there as a part of the normal beehive microbiota. This finding, in combination with its antibacterial activity against P. larvae, highlights this novel isolate as a potential natural preserving agent against AFB. Furthermore, the WGS-based approach reported here proved to be very cost- and time- efficient, for screening the applicability of new pro- and prebiotic Enterococcus strains as beehive protection agents.

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References

  1. Bansal P, Kumar R, Singh J, Dhanda S (2019) Next generation sequencing, biochemical characterization, metabolic pathway analysis of novel probiotic Pediococcusacidilactici NCDC 252 and it’s evolutionary relationship with other lactic acid bacteria. MolBiol Rep 46:5883–5895. https://doi.org/10.1007/s11033-019-05022-z

    Article  CAS  Google Scholar 

  2. Fisher K, Phillips C (2009) The ecology, epidemiology and virulence of Enterococcus. Microbiology 155:1749–1757. https://doi.org/10.1099/mic.0.026385-0

    Article  CAS  PubMed  Google Scholar 

  3. Zommiti M, Ferchichi M, Sebei K, Feuilloley MGJ, Connil N, Boukerb AM (2020) Draft Genome Sequences of Five Potentially Probiotic Enterococcus faecium Strains Isolated from an Artisanal Tunisian Meat (Dried Ossban). Microbiology Resource Announcements 9(3):e01348–e01319. https://doi.org/10.1128/MRA.01348-19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Royan M (2019) Mechanisms of Probiotic Action in the Honeybee. Crit Rev Eukaryot Gene Expr 29(2):95–103. https://doi.org/10.1615/critreveukaryotgeneexpr.2019025358

    Article  PubMed  Google Scholar 

  5. Zulkhairi AFA, SabriS, Ismail M, Chan KW, Ismail N, MohdEsaN, Mohd LilaMA, Zawawi N (2020) Probiotic Properties of Bacillus Strains Isolated from Stingless Bee (Heterotrigonaitama) Honey Collected across Malaysia. International Journal of Environmental Research Public Health 17(1):278. https://doi.org/10.3390/ijerph17010278

    Article  Google Scholar 

  6. Dimov S, Peykov S, Raykova D, Ivanova P, Kirilov N, Dalgalarrondo M, Chobert J, Haertlé T, Ivanova I (2009) A newly discovered bacteriocin produced by Enterococcus faecalis 3915. BenefMicrob 1:43–51. https://doi.org/10.3920/BM2008.1004

    Article  CAS  Google Scholar 

  7. Dimov SG (2007) A Novel Bacteriocin-Like Substance Produced by Enterococcus faecium 3587. CurrMicrobiol 55:323–327. https://doi.org/10.1007/s00284-007-0018-0

    Article  CAS  Google Scholar 

  8. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, NY, pp 115–175

    Google Scholar 

  9. Seemann T (2017) Shovill: Faster SPAdes assembly of Illumina reads on https://github.com/tseemann/shovill

  10. Afgan E, Baker D, Batut B, Van Den Beek M, Bouvier D et al (2018) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research 46(W1):W537–W544. https://doi.org/10.1093/nar/gky379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8):1072–1075. https://doi.org/10.1093/bioinformatics/btt086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. De Jong A, Van Heel AJ, Kok J, Kuipers OP (2010) BAGEL2: mining for bacteriocins in genomic data. Nucleic Acids Res 38(Web Server issue):W647-651. https://doi.org/10.1093/nar/gkq365

    Article  PubMed  PubMed Central  Google Scholar 

  13. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al (2012) Identification of acquired antimicrobial resistance genes. J AntimicrobChemother 67(11):2640–2644. https://doi.org/10.1093/jac/dks261

    Article  CAS  Google Scholar 

  14. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS et al (2014) Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenicEscherichia coli. J Clin Microbiol 52(5):1501–1510. https://doi.org/10.1128/JCM.03617-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O et al (2014) In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58(7):3895–3903. https://doi.org/10.1128/AAC.02412-14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al (2012) Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50(4):1355–1361. https://doi.org/10.1128/JCM.06094-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Jaouani I, Abbassi MS, Alessandria V, Bouraoui J, Ben Salem R, Kilani H, Mansouri R, Messadi., Cocolin L (2014) High inhibition of Paenibacillus larvae and Listeria monocytogenes by Enterococcus isolated from different sources in Tunisia and identification of their bacteriocin genes. Lett Appl Microbiol 59:17–25. https://doi.org/10.1111/lam.12239

    Article  CAS  PubMed  Google Scholar 

  18. Hollenbeck BL, Louis B. Rice LB (2012) Intrinsic and acquired resistance mechanisms in enterococcus. Virulence 3(5):421–433. https://doi.org/10.4161/viru.21282

    Article  PubMed  PubMed Central  Google Scholar 

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Funding

This study was funded by the Bulgarian National Research Fund under Grant No. КП-06-Н26/8 from 17.12.2018.

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Authors and Affiliations

  1. Faculty of Biology, Department of Genetics, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria

    Svetoslav G. Dimov, Anita Guyrova, Antoniya Vladimirova, Martin Dimitrov & Slavil Peykov

  2. Faculty of Medicine, Department of Medical Microbiology, Medical University – Sofia, Sofia, Bulgaria

    Tanya Strateva

Authors
  1. Svetoslav G. Dimov
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  2. Anita Guyrova
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  3. Antoniya Vladimirova
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  4. Martin Dimitrov
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  5. Slavil Peykov
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  6. Tanya Strateva
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Correspondence to Svetoslav G. Dimov.

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Dimov, S.G., Guyrova, A., Vladimirova, A. et al. WGS-based characterization of the potentially beneficial Enterococcus faecium EFD from a beehive. Mol Biol Rep 47, 6445–6449 (2020). https://doi.org/10.1007/s11033-020-05663-5

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  • DOI: https://doi.org/10.1007/s11033-020-05663-5

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